Query 036250
Match_columns 347
No_of_seqs 388 out of 1918
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 10:53:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036250.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036250hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14369 zf-RING_3: zinc-finge 99.6 1.3E-15 2.9E-20 100.4 3.3 33 7-39 1-35 (35)
2 KOG4628 Predicted E3 ubiquitin 99.5 3.3E-14 7.1E-19 137.8 6.8 71 193-263 203-280 (348)
3 PF13639 zf-RING_2: Ring finge 99.4 4.2E-14 9E-19 98.0 1.5 43 215-257 2-44 (44)
4 COG5243 HRD1 HRD ubiquitin lig 99.2 3.8E-11 8.2E-16 115.8 6.6 66 198-263 268-347 (491)
5 PLN03208 E3 ubiquitin-protein 99.1 4.6E-11 9.9E-16 107.3 5.3 55 209-266 14-84 (193)
6 COG5540 RING-finger-containing 99.1 2.9E-11 6.3E-16 113.9 2.6 50 213-262 323-373 (374)
7 PF12678 zf-rbx1: RING-H2 zinc 99.1 5.1E-11 1.1E-15 91.6 2.5 45 213-257 19-73 (73)
8 PHA02929 N1R/p28-like protein; 99.1 7.1E-11 1.5E-15 109.9 3.5 64 198-261 151-227 (238)
9 KOG0823 Predicted E3 ubiquitin 99.0 1.2E-10 2.6E-15 106.4 3.8 53 212-267 46-101 (230)
10 KOG0317 Predicted E3 ubiquitin 98.9 4.8E-10 1E-14 105.4 1.2 50 213-265 239-288 (293)
11 PF13920 zf-C3HC4_3: Zinc fing 98.9 9.4E-10 2E-14 78.2 2.1 46 213-261 2-48 (50)
12 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.5E-09 3.2E-14 73.2 1.8 38 216-256 1-39 (39)
13 PF15227 zf-C3HC4_4: zinc fing 98.8 2.6E-09 5.6E-14 73.4 2.0 38 216-256 1-42 (42)
14 cd00162 RING RING-finger (Real 98.8 3.8E-09 8.2E-14 71.6 2.4 43 215-260 1-45 (45)
15 smart00504 Ubox Modified RING 98.7 4.7E-09 1E-13 77.5 2.4 49 214-265 2-50 (63)
16 KOG0802 E3 ubiquitin ligase [P 98.7 8E-09 1.7E-13 107.4 1.8 50 213-262 291-342 (543)
17 KOG0320 Predicted E3 ubiquitin 98.6 1.1E-08 2.4E-13 90.1 1.1 50 214-264 132-181 (187)
18 TIGR00599 rad18 DNA repair pro 98.6 1.8E-08 4E-13 100.2 2.6 51 210-263 23-73 (397)
19 PF00097 zf-C3HC4: Zinc finger 98.6 1.8E-08 3.9E-13 68.3 1.6 38 216-256 1-41 (41)
20 smart00184 RING Ring finger. E 98.6 2.6E-08 5.7E-13 65.1 1.9 38 216-256 1-39 (39)
21 PF14634 zf-RING_5: zinc-RING 98.5 3.1E-08 6.8E-13 68.6 1.8 44 215-258 1-44 (44)
22 PF12861 zf-Apc11: Anaphase-pr 98.5 4.7E-08 1E-12 76.8 2.0 50 212-261 20-82 (85)
23 PHA02926 zinc finger-like prot 98.5 6E-08 1.3E-12 88.5 1.6 50 212-261 169-230 (242)
24 KOG0287 Postreplication repair 98.4 8.5E-08 1.8E-12 91.9 1.3 53 211-266 21-73 (442)
25 KOG2164 Predicted E3 ubiquitin 98.4 7.8E-08 1.7E-12 96.8 1.0 55 212-269 185-244 (513)
26 COG5574 PEX10 RING-finger-cont 98.3 1.4E-07 3E-12 88.0 0.6 50 212-264 214-265 (271)
27 PF04564 U-box: U-box domain; 98.3 3E-07 6.4E-12 70.6 1.6 51 212-265 3-54 (73)
28 KOG1734 Predicted RING-contain 98.3 2.3E-07 4.9E-12 86.6 0.5 64 204-268 216-288 (328)
29 PF13445 zf-RING_UBOX: RING-ty 98.2 4E-07 8.6E-12 62.9 1.5 38 216-254 1-43 (43)
30 COG5194 APC11 Component of SCF 98.2 7.4E-07 1.6E-11 68.6 1.9 49 214-262 21-82 (88)
31 COG5432 RAD18 RING-finger-cont 98.1 1.2E-06 2.7E-11 82.6 1.9 48 212-262 24-71 (391)
32 smart00744 RINGv The RING-vari 98.1 1.6E-06 3.5E-11 61.5 1.7 42 215-257 1-49 (49)
33 KOG2930 SCF ubiquitin ligase, 98.0 2.7E-06 5.8E-11 68.6 2.5 48 213-260 46-107 (114)
34 KOG2177 Predicted E3 ubiquitin 98.0 1.9E-06 4.2E-11 79.9 1.7 46 210-258 10-55 (386)
35 KOG0804 Cytoplasmic Zn-finger 98.0 3E-06 6.5E-11 84.2 2.4 54 206-261 168-222 (493)
36 KOG0828 Predicted E3 ubiquitin 98.0 1.7E-06 3.6E-11 86.7 0.2 50 213-262 571-635 (636)
37 PF14835 zf-RING_6: zf-RING of 98.0 2.1E-06 4.6E-11 63.8 0.7 52 211-267 5-57 (65)
38 COG5219 Uncharacterized conser 98.0 3E-06 6.5E-11 90.2 1.8 53 207-261 1463-1523(1525)
39 KOG1493 Anaphase-promoting com 97.9 1.2E-06 2.6E-11 66.9 -1.4 49 213-261 20-81 (84)
40 PF11793 FANCL_C: FANCL C-term 97.8 4.3E-06 9.3E-11 63.8 -0.2 50 213-262 2-67 (70)
41 TIGR00570 cdk7 CDK-activating 97.8 1.2E-05 2.6E-10 77.4 2.3 54 213-266 3-59 (309)
42 KOG4265 Predicted E3 ubiquitin 97.7 1.5E-05 3.3E-10 77.5 1.5 47 213-262 290-337 (349)
43 KOG0311 Predicted E3 ubiquitin 97.7 7.8E-06 1.7E-10 79.2 -0.6 51 210-263 40-92 (381)
44 KOG0824 Predicted E3 ubiquitin 97.6 1.6E-05 3.6E-10 75.5 1.2 48 214-264 8-56 (324)
45 KOG4445 Uncharacterized conser 97.5 2.2E-05 4.7E-10 74.6 0.2 91 176-267 76-192 (368)
46 KOG0825 PHD Zn-finger protein 97.4 4.1E-05 8.8E-10 80.5 0.6 54 213-266 123-176 (1134)
47 KOG1785 Tyrosine kinase negati 97.4 0.00011 2.3E-09 72.4 3.4 50 215-267 371-422 (563)
48 KOG0827 Predicted E3 ubiquitin 97.3 7.6E-05 1.7E-09 73.1 0.4 49 214-262 5-57 (465)
49 KOG4172 Predicted E3 ubiquitin 97.2 3.9E-05 8.4E-10 55.1 -1.5 45 214-261 8-54 (62)
50 KOG0978 E3 ubiquitin ligase in 97.1 8.6E-05 1.9E-09 78.3 -0.6 51 212-265 642-693 (698)
51 KOG4159 Predicted E3 ubiquitin 97.1 0.00021 4.6E-09 71.5 2.0 49 211-262 82-130 (398)
52 KOG1039 Predicted E3 ubiquitin 97.1 0.00032 6.9E-09 68.9 2.5 54 208-261 156-221 (344)
53 KOG0297 TNF receptor-associate 96.9 0.00036 7.8E-09 70.0 1.5 52 210-264 18-70 (391)
54 KOG2660 Locus-specific chromos 96.8 0.00033 7.1E-09 67.6 -0.2 50 211-263 13-63 (331)
55 KOG1645 RING-finger-containing 96.6 0.00073 1.6E-08 66.8 1.4 48 213-260 4-55 (463)
56 PF11789 zf-Nse: Zinc-finger o 96.5 0.0015 3.2E-08 47.8 1.6 40 213-255 11-53 (57)
57 COG5152 Uncharacterized conser 96.3 0.0012 2.5E-08 59.7 0.2 44 214-260 197-240 (259)
58 KOG1941 Acetylcholine receptor 96.2 0.0014 3E-08 64.5 0.6 48 213-260 365-415 (518)
59 KOG3970 Predicted E3 ubiquitin 96.0 0.0036 7.8E-08 57.6 1.8 52 213-265 50-109 (299)
60 PF05883 Baculo_RING: Baculovi 95.8 0.0037 8.1E-08 53.3 1.2 35 213-247 26-66 (134)
61 KOG0801 Predicted E3 ubiquitin 95.6 0.0026 5.5E-08 55.8 -0.6 28 213-240 177-204 (205)
62 KOG1571 Predicted E3 ubiquitin 95.6 0.0045 9.8E-08 60.6 1.0 45 211-261 303-347 (355)
63 KOG1002 Nucleotide excision re 95.5 0.0036 7.8E-08 63.9 -0.1 50 212-264 535-589 (791)
64 KOG1813 Predicted E3 ubiquitin 95.5 0.0041 8.8E-08 59.4 0.2 46 214-262 242-287 (313)
65 COG5222 Uncharacterized conser 95.4 0.0074 1.6E-07 57.7 1.5 46 214-262 275-323 (427)
66 PF10367 Vps39_2: Vacuolar sor 95.4 0.0062 1.3E-07 49.2 0.9 37 207-244 72-108 (109)
67 KOG1428 Inhibitor of type V ad 95.2 0.009 2E-07 66.9 1.6 50 212-261 3485-3544(3738)
68 COG0375 HybF Zn finger protein 95.1 0.014 3.1E-07 48.6 2.4 36 6-42 68-103 (115)
69 PF12906 RINGv: RING-variant d 95.1 0.013 2.9E-07 41.1 1.9 40 216-256 1-47 (47)
70 KOG4692 Predicted E3 ubiquitin 95.1 0.01 2.2E-07 58.0 1.7 49 211-262 420-468 (489)
71 KOG2879 Predicted E3 ubiquitin 95.1 0.012 2.6E-07 55.7 2.1 47 212-261 238-287 (298)
72 KOG1814 Predicted E3 ubiquitin 94.9 0.0096 2.1E-07 59.2 0.8 46 213-258 184-237 (445)
73 KOG4275 Predicted E3 ubiquitin 94.4 0.011 2.4E-07 56.3 -0.0 42 213-261 300-342 (350)
74 PF14570 zf-RING_4: RING/Ubox 94.2 0.017 3.7E-07 40.7 0.6 44 216-260 1-47 (48)
75 KOG0826 Predicted E3 ubiquitin 94.1 0.037 8.1E-07 53.7 2.9 47 213-262 300-347 (357)
76 PF14447 Prok-RING_4: Prokaryo 93.7 0.033 7.1E-07 40.3 1.3 45 215-264 9-53 (55)
77 KOG1952 Transcription factor N 93.4 0.027 5.9E-07 60.5 0.7 48 212-259 190-245 (950)
78 KOG0827 Predicted E3 ubiquitin 93.4 0.0069 1.5E-07 59.8 -3.5 50 214-263 197-247 (465)
79 KOG4739 Uncharacterized protei 93.4 0.027 5.9E-07 52.4 0.6 47 215-264 5-51 (233)
80 PHA02862 5L protein; Provision 93.3 0.029 6.4E-07 48.4 0.6 45 214-262 3-54 (156)
81 KOG3268 Predicted E3 ubiquitin 93.0 0.038 8.2E-07 49.3 0.8 50 214-263 166-230 (234)
82 KOG0298 DEAD box-containing he 92.9 0.076 1.6E-06 59.5 3.1 82 173-258 1115-1196(1394)
83 KOG3039 Uncharacterized conser 92.7 0.084 1.8E-06 49.4 2.7 54 214-267 222-276 (303)
84 PF08746 zf-RING-like: RING-li 92.4 0.033 7E-07 38.4 -0.4 41 216-256 1-43 (43)
85 PF10272 Tmpp129: Putative tra 92.2 0.12 2.7E-06 51.2 3.3 31 234-264 311-354 (358)
86 COG5236 Uncharacterized conser 92.1 0.07 1.5E-06 52.2 1.4 47 211-260 59-107 (493)
87 KOG1940 Zn-finger protein [Gen 92.0 0.084 1.8E-06 50.5 1.8 45 214-258 159-204 (276)
88 TIGR00100 hypA hydrogenase nic 91.6 0.17 3.6E-06 42.2 3.0 35 6-41 68-102 (115)
89 PF07754 DUF1610: Domain of un 91.3 0.11 2.3E-06 31.4 1.1 22 11-32 1-23 (24)
90 PHA03096 p28-like protein; Pro 91.2 0.088 1.9E-06 50.7 1.1 45 214-258 179-231 (284)
91 PHA02825 LAP/PHD finger-like p 90.9 0.1 2.2E-06 45.8 1.1 47 213-263 8-61 (162)
92 KOG4185 Predicted E3 ubiquitin 90.9 0.099 2.1E-06 50.2 1.1 47 214-260 4-54 (296)
93 PRK03681 hypA hydrogenase nick 90.4 0.21 4.6E-06 41.6 2.5 36 6-41 68-103 (114)
94 KOG1001 Helicase-like transcri 90.2 0.082 1.8E-06 56.7 -0.1 50 214-267 455-506 (674)
95 PRK12380 hydrogenase nickel in 90.2 0.22 4.9E-06 41.4 2.5 34 6-40 68-101 (113)
96 KOG2114 Vacuolar assembly/sort 90.0 0.12 2.5E-06 55.8 0.8 43 213-260 840-882 (933)
97 PF07800 DUF1644: Protein of u 89.7 0.22 4.8E-06 43.7 2.1 32 213-247 2-46 (162)
98 PRK00564 hypA hydrogenase nick 89.5 0.3 6.5E-06 40.9 2.7 36 6-41 69-104 (117)
99 PF04641 Rtf2: Rtf2 RING-finge 89.4 0.22 4.8E-06 47.3 2.1 53 213-266 113-166 (260)
100 KOG2932 E3 ubiquitin ligase in 89.3 0.12 2.7E-06 49.8 0.4 42 215-260 92-133 (389)
101 PF01155 HypA: Hydrogenase exp 89.0 0.2 4.3E-06 41.6 1.3 34 6-40 68-101 (113)
102 PF05290 Baculo_IE-1: Baculovi 88.2 0.15 3.3E-06 43.5 0.1 47 214-263 81-134 (140)
103 COG2093 DNA-directed RNA polym 88.1 0.23 4.9E-06 36.9 1.0 28 10-40 6-34 (64)
104 KOG2817 Predicted E3 ubiquitin 87.9 0.34 7.4E-06 48.3 2.3 48 212-259 333-383 (394)
105 KOG4367 Predicted Zn-finger pr 87.3 0.23 5E-06 50.0 0.8 36 211-249 2-37 (699)
106 COG1996 RPC10 DNA-directed RNA 86.9 0.43 9.2E-06 33.9 1.7 29 6-34 4-33 (49)
107 KOG2034 Vacuolar sorting prote 86.8 0.28 6E-06 53.3 1.1 37 210-247 814-850 (911)
108 KOG1100 Predicted E3 ubiquitin 86.7 0.31 6.7E-06 44.9 1.3 39 216-261 161-200 (207)
109 smart00659 RPOLCX RNA polymera 86.2 0.62 1.4E-05 32.2 2.2 29 8-36 2-30 (44)
110 PRK03824 hypA hydrogenase nick 86.1 0.57 1.2E-05 40.2 2.5 35 6-40 68-122 (135)
111 PF14446 Prok-RING_1: Prokaryo 85.9 0.47 1E-05 34.3 1.6 38 214-255 6-44 (54)
112 KOG3002 Zn finger protein [Gen 85.6 0.53 1.1E-05 45.7 2.3 45 210-261 45-91 (299)
113 PF03854 zf-P11: P-11 zinc fin 85.3 0.26 5.6E-06 34.7 -0.0 33 231-263 15-48 (50)
114 KOG3161 Predicted E3 ubiquitin 84.7 0.38 8.1E-06 50.7 0.8 44 213-259 11-55 (861)
115 PRK00762 hypA hydrogenase nick 83.4 0.88 1.9E-05 38.4 2.4 35 6-41 68-108 (124)
116 PF03604 DNA_RNApol_7kD: DNA d 82.3 1.1 2.3E-05 29.0 1.9 25 9-33 1-25 (32)
117 PRK00398 rpoP DNA-directed RNA 81.9 1.4 3E-05 30.4 2.6 32 7-38 2-34 (46)
118 KOG0309 Conserved WD40 repeat- 81.8 0.47 1E-05 50.8 0.2 30 226-255 1040-1069(1081)
119 KOG0802 E3 ubiquitin ligase [P 81.6 1.1 2.4E-05 47.0 2.8 47 213-266 479-525 (543)
120 KOG3800 Predicted E3 ubiquitin 79.2 1.1 2.3E-05 43.1 1.6 53 215-267 2-57 (300)
121 KOG4317 Predicted Zn-finger pr 77.5 1.4 3E-05 42.8 1.8 27 4-35 3-29 (383)
122 smart00834 CxxC_CXXC_SSSS Puta 75.2 2.7 5.8E-05 27.8 2.3 26 8-33 5-34 (41)
123 COG5175 MOT2 Transcriptional r 74.7 1.3 2.8E-05 43.5 0.8 55 212-266 13-69 (480)
124 KOG3993 Transcription factor ( 74.4 1.4 3.1E-05 44.4 1.1 22 12-37 286-307 (500)
125 KOG4362 Transcriptional regula 74.3 0.58 1.3E-05 49.9 -1.7 47 213-262 21-70 (684)
126 PF06906 DUF1272: Protein of u 73.2 1.2 2.5E-05 32.5 0.1 32 4-37 22-53 (57)
127 KOG3899 Uncharacterized conser 72.7 1.2 2.6E-05 42.9 0.1 32 234-265 325-369 (381)
128 COG5270 PUA domain (predicted 72.2 2.2 4.7E-05 38.5 1.6 28 6-38 12-39 (202)
129 PF02891 zf-MIZ: MIZ/SP-RING z 71.4 3 6.5E-05 29.5 1.9 43 214-259 3-50 (50)
130 KOG0825 PHD Zn-finger protein 70.8 1.7 3.6E-05 47.0 0.6 49 214-262 97-155 (1134)
131 COG5183 SSM4 Protein involved 70.1 1.6 3.5E-05 47.2 0.4 51 213-264 12-69 (1175)
132 KOG0269 WD40 repeat-containing 68.9 2.6 5.7E-05 45.4 1.6 44 214-258 780-825 (839)
133 KOG1609 Protein involved in mR 68.6 1.4 3E-05 42.1 -0.4 50 214-263 79-136 (323)
134 PF13240 zinc_ribbon_2: zinc-r 68.6 2.3 4.9E-05 25.3 0.6 22 10-34 1-22 (23)
135 PF10571 UPF0547: Uncharacteri 68.2 2.8 6.2E-05 25.7 1.0 23 11-36 3-25 (26)
136 KOG1812 Predicted E3 ubiquitin 67.8 1.8 3.9E-05 43.6 0.1 38 213-250 146-184 (384)
137 PF08792 A2L_zn_ribbon: A2L zi 65.0 3.7 8E-05 26.6 1.2 27 9-35 4-31 (33)
138 KOG4718 Non-SMC (structural ma 62.5 5 0.00011 37.0 1.9 43 214-258 182-224 (235)
139 COG5109 Uncharacterized conser 60.7 5.3 0.00011 39.0 1.8 45 213-257 336-383 (396)
140 PRK06266 transcription initiat 60.6 6.6 0.00014 35.3 2.4 32 6-37 115-148 (178)
141 COG5220 TFB3 Cdk activating ki 59.4 3.5 7.5E-05 38.8 0.3 49 213-261 10-64 (314)
142 PF07860 CCD: WisP family C-Te 59.2 5.4 0.00012 32.7 1.4 34 299-339 49-82 (141)
143 PF09723 Zn-ribbon_8: Zinc rib 57.3 10 0.00022 25.7 2.3 27 8-34 5-35 (42)
144 PF08772 NOB1_Zn_bind: Nin one 56.6 6.9 0.00015 30.1 1.5 30 9-40 10-39 (73)
145 smart00661 RPOL9 RNA polymeras 56.6 6.7 0.00015 27.3 1.4 29 10-40 2-33 (52)
146 KOG1812 Predicted E3 ubiquitin 55.7 5.4 0.00012 40.1 1.1 43 214-256 307-351 (384)
147 KOG3579 Predicted E3 ubiquitin 55.4 9.6 0.00021 36.7 2.6 38 213-251 268-307 (352)
148 KOG2066 Vacuolar assembly/sort 54.3 5 0.00011 43.5 0.6 46 210-256 781-830 (846)
149 PF14803 Nudix_N_2: Nudix N-te 53.3 5.4 0.00012 26.1 0.4 23 10-32 2-29 (34)
150 TIGR00373 conserved hypothetic 52.0 9.3 0.0002 33.6 1.8 34 6-40 107-142 (158)
151 PF13248 zf-ribbon_3: zinc-rib 51.8 7 0.00015 23.7 0.7 23 9-34 3-25 (26)
152 PF05605 zf-Di19: Drought indu 50.8 8.6 0.00019 27.3 1.2 11 25-35 2-12 (54)
153 PF03811 Zn_Tnp_IS1: InsA N-te 50.2 7.2 0.00016 25.8 0.6 10 25-34 5-14 (36)
154 cd00730 rubredoxin Rubredoxin; 49.7 14 0.0003 26.3 2.0 26 8-33 1-42 (50)
155 KOG3053 Uncharacterized conser 49.5 4.1 8.8E-05 38.6 -0.9 50 213-262 20-83 (293)
156 PRK06393 rpoE DNA-directed RNA 49.3 9 0.00019 28.7 1.1 18 11-33 8-25 (64)
157 KOG3039 Uncharacterized conser 48.4 7.9 0.00017 36.6 0.8 32 214-248 44-75 (303)
158 TIGR02605 CxxC_CxxC_SSSS putat 47.7 20 0.00044 24.9 2.7 32 8-39 5-40 (52)
159 PF03107 C1_2: C1 domain; Int 47.6 7.3 0.00016 24.4 0.3 22 9-32 1-22 (30)
160 PF00301 Rubredoxin: Rubredoxi 47.1 17 0.00037 25.5 2.1 27 8-34 1-43 (47)
161 PRK14890 putative Zn-ribbon RN 46.9 14 0.00031 27.2 1.8 22 10-31 9-31 (59)
162 KOG2807 RNA polymerase II tran 46.6 14 0.0003 36.3 2.2 46 213-258 330-375 (378)
163 PRK08351 DNA-directed RNA poly 46.3 11 0.00025 27.9 1.2 19 10-33 5-23 (61)
164 PF10122 Mu-like_Com: Mu-like 46.0 6.7 0.00014 28.0 -0.0 28 7-34 3-33 (51)
165 smart00531 TFIIE Transcription 45.9 18 0.00038 31.3 2.6 33 6-38 97-136 (147)
166 smart00132 LIM Zinc-binding do 45.4 16 0.00034 23.0 1.7 36 216-260 2-37 (39)
167 PF13901 DUF4206: Domain of un 44.5 13 0.00028 33.9 1.7 41 213-258 152-197 (202)
168 KOG2068 MOT2 transcription fac 44.3 14 0.00029 36.4 1.8 49 214-262 250-299 (327)
169 KOG1815 Predicted E3 ubiquitin 44.3 7.1 0.00015 39.9 -0.1 36 212-249 69-104 (444)
170 TIGR00155 pqiA_fam integral me 43.6 13 0.00028 37.7 1.5 24 10-35 217-240 (403)
171 COG3813 Uncharacterized protei 43.6 7.6 0.00017 29.8 -0.0 33 4-38 22-54 (84)
172 PF08271 TF_Zn_Ribbon: TFIIB z 42.5 15 0.00032 24.9 1.2 13 26-38 1-13 (43)
173 KOG3005 GIY-YIG type nuclease 42.4 17 0.00037 34.7 2.1 50 214-263 183-245 (276)
174 PRK12495 hypothetical protein; 41.9 14 0.0003 34.3 1.4 32 4-36 38-69 (226)
175 smart00154 ZnF_AN1 AN1-like Zi 41.5 15 0.00032 24.6 1.1 25 11-38 1-25 (39)
176 KOG1729 FYVE finger containing 41.4 13 0.00029 35.9 1.2 37 214-250 215-251 (288)
177 PF00412 LIM: LIM domain; Int 41.3 16 0.00036 25.5 1.4 40 216-264 1-40 (58)
178 PF14968 CCDC84: Coiled coil p 39.8 14 0.00031 36.5 1.2 34 4-42 54-87 (336)
179 PHA00616 hypothetical protein 39.4 8 0.00017 26.8 -0.5 12 26-37 2-13 (44)
180 COG4391 Uncharacterized protei 39.0 13 0.00028 27.6 0.6 13 24-36 47-59 (62)
181 KOG1829 Uncharacterized conser 38.6 8.9 0.00019 40.6 -0.5 42 213-257 511-557 (580)
182 COG5151 SSL1 RNA polymerase II 38.1 18 0.00038 35.4 1.5 26 6-34 306-331 (421)
183 PF13719 zinc_ribbon_5: zinc-r 37.9 14 0.00031 24.3 0.6 11 26-36 3-13 (37)
184 cd00350 rubredoxin_like Rubred 37.2 34 0.00074 21.8 2.3 25 8-33 1-25 (33)
185 PF15135 UPF0515: Uncharacteri 37.0 16 0.00035 34.6 1.0 26 11-36 135-166 (278)
186 smart00647 IBR In Between Ring 36.8 23 0.00051 25.2 1.7 34 6-39 16-54 (64)
187 PF06677 Auto_anti-p27: Sjogre 36.6 27 0.00058 23.8 1.8 23 10-32 19-41 (41)
188 PF09538 FYDLN_acid: Protein o 36.0 28 0.00061 28.7 2.2 33 6-38 7-39 (108)
189 PF06844 DUF1244: Protein of u 35.8 15 0.00032 27.7 0.4 12 237-248 11-22 (68)
190 PF07975 C1_4: TFIIH C1-like d 35.6 16 0.00034 26.2 0.5 29 10-38 1-34 (51)
191 PF01363 FYVE: FYVE zinc finge 34.5 27 0.00059 25.6 1.8 35 213-247 9-44 (69)
192 KOG2807 RNA polymerase II tran 34.2 29 0.00063 34.2 2.3 29 5-36 273-301 (378)
193 smart00249 PHD PHD zinc finger 33.7 17 0.00036 23.7 0.4 30 216-245 2-31 (47)
194 cd07973 Spt4 Transcription elo 33.1 23 0.0005 28.8 1.2 26 11-37 6-31 (98)
195 PF00096 zf-C2H2: Zinc finger, 32.6 10 0.00022 21.6 -0.7 11 26-36 1-11 (23)
196 PF06906 DUF1272: Protein of u 32.3 38 0.00083 24.7 2.1 46 215-262 7-53 (57)
197 PF14353 CpXC: CpXC protein 32.2 26 0.00057 29.2 1.5 18 25-42 1-18 (128)
198 COG2888 Predicted Zn-ribbon RN 32.1 41 0.00089 24.9 2.2 27 6-32 25-57 (61)
199 PF14787 zf-CCHC_5: GAG-polypr 31.9 23 0.0005 23.5 0.8 11 26-36 3-13 (36)
200 PF00628 PHD: PHD-finger; Int 31.8 22 0.00048 24.4 0.8 43 215-257 1-49 (51)
201 TIGR00686 phnA alkylphosphonat 31.4 25 0.00054 29.1 1.1 28 11-38 5-32 (109)
202 PRK10220 hypothetical protein; 31.3 27 0.00059 28.9 1.3 28 11-38 6-33 (111)
203 PF04216 FdhE: Protein involve 31.2 8.7 0.00019 36.9 -1.9 45 213-258 172-219 (290)
204 TIGR02300 FYDLN_acid conserved 30.4 39 0.00085 28.8 2.2 33 6-38 7-39 (129)
205 PF13913 zf-C2HC_2: zinc-finge 30.4 16 0.00035 21.9 -0.1 13 26-38 3-15 (25)
206 TIGR00155 pqiA_fam integral me 30.3 27 0.00058 35.4 1.4 26 10-35 15-43 (403)
207 TIGR02098 MJ0042_CXXC MJ0042 f 30.2 44 0.00096 21.6 2.0 28 9-36 3-36 (38)
208 PF13465 zf-H2C2_2: Zinc-finge 29.4 12 0.00026 22.5 -0.8 11 26-36 15-25 (26)
209 PF03966 Trm112p: Trm112p-like 29.2 20 0.00044 26.7 0.3 14 22-35 50-63 (68)
210 COG1066 Sms Predicted ATP-depe 29.2 52 0.0011 33.7 3.2 39 1-43 1-41 (456)
211 TIGR01384 TFS_arch transcripti 29.1 26 0.00056 28.1 0.9 24 10-34 2-25 (104)
212 PF12760 Zn_Tnp_IS1595: Transp 28.7 33 0.00072 23.5 1.2 12 23-34 16-27 (46)
213 KOG2169 Zn-finger transcriptio 28.3 50 0.0011 35.5 3.1 44 214-264 307-359 (636)
214 PF04438 zf-HIT: HIT zinc fing 28.1 40 0.00086 21.3 1.4 21 8-34 2-22 (30)
215 KOG4185 Predicted E3 ubiquitin 28.1 18 0.00039 34.5 -0.2 46 214-259 208-265 (296)
216 PF13453 zf-TFIIB: Transcripti 27.9 24 0.00052 23.6 0.4 27 11-37 2-31 (41)
217 KOG3113 Uncharacterized conser 27.7 39 0.00085 32.2 1.9 52 214-267 112-164 (293)
218 PRK00432 30S ribosomal protein 27.6 29 0.00064 24.5 0.8 13 26-38 21-33 (50)
219 PRK13794 hypothetical protein; 26.9 34 0.00073 35.5 1.5 29 7-40 9-38 (479)
220 COG1867 TRM1 N2,N2-dimethylgua 26.2 43 0.00094 33.6 2.0 30 6-35 238-267 (380)
221 PF07191 zinc-ribbons_6: zinc- 26.0 32 0.00069 26.3 0.8 13 7-19 16-28 (70)
222 COG1198 PriA Primosomal protei 25.9 42 0.00091 36.7 2.0 32 6-41 460-491 (730)
223 PRK15103 paraquat-inducible me 25.7 39 0.00084 34.4 1.7 23 10-35 223-245 (419)
224 PF07282 OrfB_Zn_ribbon: Putat 25.2 35 0.00076 25.1 0.9 23 10-32 30-53 (69)
225 TIGR00622 ssl1 transcription f 25.2 61 0.0013 27.0 2.4 43 215-257 57-110 (112)
226 PHA02776 E7 protein; Provision 25.0 31 0.00067 28.2 0.6 27 7-33 53-99 (101)
227 KOG1815 Predicted E3 ubiquitin 25.0 25 0.00053 36.0 0.1 37 214-250 227-268 (444)
228 PF00527 E7: E7 protein, Early 24.6 30 0.00065 27.7 0.5 25 7-31 47-91 (92)
229 PF13894 zf-C2H2_4: C2H2-type 24.3 25 0.00054 19.5 -0.0 10 26-35 1-10 (24)
230 PHA00626 hypothetical protein 24.1 59 0.0013 23.8 1.8 29 11-39 3-37 (59)
231 PLN02189 cellulose synthase 24.1 72 0.0016 36.2 3.4 48 214-261 35-87 (1040)
232 PF11261 IRF-2BP1_2: Interfero 24.0 35 0.00076 24.4 0.7 25 7-31 2-30 (54)
233 PF04710 Pellino: Pellino; In 23.8 26 0.00057 35.3 0.0 28 232-259 307-337 (416)
234 PF12773 DZR: Double zinc ribb 23.8 39 0.00085 23.2 0.9 26 8-33 12-37 (50)
235 KOG2113 Predicted RNA binding 23.7 56 0.0012 32.1 2.2 48 208-260 338-386 (394)
236 smart00109 C1 Protein kinase C 23.3 48 0.001 22.0 1.3 24 8-32 11-34 (49)
237 TIGR00622 ssl1 transcription f 23.2 45 0.00097 27.8 1.3 21 9-32 2-22 (112)
238 PF07649 C1_3: C1-like domain; 23.1 30 0.00065 21.4 0.2 23 9-33 1-23 (30)
239 COG4416 Com Mu-like prophage p 23.0 33 0.00072 24.8 0.4 26 8-33 4-32 (60)
240 PF05191 ADK_lid: Adenylate ki 22.9 81 0.0018 20.7 2.2 30 8-37 1-33 (36)
241 COG2995 PqiA Uncharacterized p 22.8 37 0.00081 34.3 0.8 24 8-33 220-243 (418)
242 PF08274 PhnA_Zn_Ribbon: PhnA 22.4 35 0.00075 21.7 0.4 23 11-33 5-27 (30)
243 PF04423 Rad50_zn_hook: Rad50 22.3 32 0.00069 24.3 0.2 12 252-263 22-33 (54)
244 KOG2932 E3 ubiquitin ligase in 22.0 33 0.00072 33.6 0.3 26 8-33 90-131 (389)
245 COG1885 Uncharacterized protei 21.9 59 0.0013 26.7 1.7 18 18-36 43-60 (115)
246 PRK11823 DNA repair protein Ra 21.9 69 0.0015 32.8 2.6 31 6-39 5-37 (446)
247 TIGR02159 PA_CoA_Oxy4 phenylac 21.8 53 0.0011 28.5 1.5 17 25-41 105-121 (146)
248 KOG0824 Predicted E3 ubiquitin 21.7 99 0.0021 30.2 3.4 48 213-262 105-152 (324)
249 PF02701 zf-Dof: Dof domain, z 21.7 44 0.00095 24.9 0.8 9 25-33 5-13 (63)
250 PRK00420 hypothetical protein; 21.7 56 0.0012 27.2 1.6 27 9-35 24-50 (112)
251 KOG3799 Rab3 effector RIM1 and 21.6 42 0.00092 28.9 0.8 52 208-259 60-116 (169)
252 TIGR01206 lysW lysine biosynth 21.3 54 0.0012 23.7 1.2 30 8-37 2-34 (54)
253 PRK15103 paraquat-inducible me 21.2 54 0.0012 33.4 1.6 26 10-35 12-40 (419)
254 PRK04338 N(2),N(2)-dimethylgua 21.1 79 0.0017 31.7 2.8 30 7-36 243-272 (382)
255 PF01485 IBR: IBR domain; Int 20.7 56 0.0012 23.1 1.3 27 9-35 19-50 (64)
256 COG1645 Uncharacterized Zn-fin 20.6 52 0.0011 28.2 1.2 29 7-36 27-55 (131)
257 PF14569 zf-UDP: Zinc-binding 20.3 65 0.0014 25.1 1.5 48 214-261 10-62 (80)
258 PRK06260 threonine synthase; V 20.1 70 0.0015 32.1 2.2 26 8-34 3-28 (397)
No 1
>PF14369 zf-RING_3: zinc-finger
Probab=99.57 E-value=1.3e-15 Score=100.41 Aligned_cols=33 Identities=39% Similarity=1.040 Sum_probs=28.0
Q ss_pred CcEeeecCCceeeecC--CCCccCCCCCCCceEec
Q 036250 7 GSYWCYICSRMVNPRM--EAGIKCPFCETGFVEQM 39 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~--~~e~~CP~C~sGFiEE~ 39 (347)
++||||+|++.|++.. .++++||+|++||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 5899999999999753 33455999999999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.49 E-value=3.3e-14 Score=137.79 Aligned_cols=71 Identities=35% Similarity=0.852 Sum_probs=61.2
Q ss_pred CCCcchHHHHHcCCcccccc---c---ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC-CCCCCCcccCCC
Q 036250 193 GSLPAQKEVVKALPTVAIDQ---D---LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS-SCPICRYQLPSD 263 (347)
Q Consensus 193 ~~~p~~~~~i~~lp~~~~~~---~---~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~ 263 (347)
......|..++++|...+.. . ..|+||+|+|+.|++++.|||+|.||..||++||..+. .||+||+.+...
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 44567799999999987754 1 28999999999999999999999999999999998775 599999977654
No 3
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.42 E-value=4.2e-14 Score=98.00 Aligned_cols=43 Identities=49% Similarity=1.239 Sum_probs=40.4
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCC
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (347)
+|+||++.|..++.++.++|+|.||..||..|++.+.+||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 6999999999889999999999999999999999999999997
No 4
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.17 E-value=3.8e-11 Score=115.75 Aligned_cols=66 Identities=35% Similarity=0.786 Sum_probs=51.9
Q ss_pred hHHHHHcCCccccc----ccccchhhhhhh-ccC---------CceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250 198 QKEVVKALPTVAID----QDLQCAVCLEEF-VMG---------NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD 263 (347)
Q Consensus 198 ~~~~i~~lp~~~~~----~~~~C~ICl~~~-~~~---------~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (347)
.|+.-+.+|++..+ ++..|.||+|++ +.+ .++++|||||++|.+|++-|++++.+||+||.++.-+
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 34444555655544 367999999994 332 3689999999999999999999999999999996444
No 5
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.14 E-value=4.6e-11 Score=107.26 Aligned_cols=55 Identities=25% Similarity=0.690 Sum_probs=45.6
Q ss_pred cccccccchhhhhhhccCCceEEecCCCcccccchHHHHhc----------------CCCCCCCCcccCCCCCc
Q 036250 209 AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL----------------QSSCPICRYQLPSDDLK 266 (347)
Q Consensus 209 ~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~~~ 266 (347)
...++.+|+||++.+ .+++.++|+|+||+.||.+|+.. ...||+||..+...+..
T Consensus 14 ~~~~~~~CpICld~~---~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 14 DSGGDFDCNICLDQV---RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred cCCCccCCccCCCcC---CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 334567999999999 77889999999999999999852 24699999999776554
No 6
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.11 E-value=2.9e-11 Score=113.88 Aligned_cols=50 Identities=34% Similarity=1.079 Sum_probs=46.4
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~ 262 (347)
..+|+||++.|..+++.+.|||.|.||..||.+|+. .+..||+||.+++.
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 469999999999999999999999999999999997 67789999999875
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=5.1e-11 Score=91.63 Aligned_cols=45 Identities=40% Similarity=0.870 Sum_probs=36.1
Q ss_pred cccchhhhhhhcc----------CCceEEecCCCcccccchHHHHhcCCCCCCCC
Q 036250 213 DLQCAVCLEEFVM----------GNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257 (347)
Q Consensus 213 ~~~C~ICl~~~~~----------~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (347)
+..|+||++.|.. ...+...+|+|.||..||.+||+.+.+||+||
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 3469999999932 22345667999999999999999999999998
No 8
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.07 E-value=7.1e-11 Score=109.91 Aligned_cols=64 Identities=31% Similarity=0.687 Sum_probs=50.4
Q ss_pred hHHHHHcCCccccc--------ccccchhhhhhhccCC-----ceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250 198 QKEVVKALPTVAID--------QDLQCAVCLEEFVMGN-----EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 198 ~~~~i~~lp~~~~~--------~~~~C~ICl~~~~~~~-----~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
.+..++.+|.+..+ .+.+|+||++.+.... -++.++|+|.||..||.+|+..+.+||+||..+.
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 56777788876422 3578999999985432 1345579999999999999999999999999875
No 9
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.04 E-value=1.2e-10 Score=106.43 Aligned_cols=53 Identities=25% Similarity=0.699 Sum_probs=45.3
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC---CCCCCCCcccCCCCCcc
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQLPSDDLKV 267 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~~~~~ 267 (347)
...+|.||||.- ++++++.|||+||+.||.+||..+ ..||+||..+..++...
T Consensus 46 ~~FdCNICLd~a---kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP 101 (230)
T KOG0823|consen 46 GFFDCNICLDLA---KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP 101 (230)
T ss_pred Cceeeeeecccc---CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence 356999999998 889999999999999999999754 35999999998776543
No 10
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=4.8e-10 Score=105.39 Aligned_cols=50 Identities=30% Similarity=0.856 Sum_probs=45.4
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (347)
...|.+||+.. .++.-+||||+||+.||..|+..+..||+||..+...+.
T Consensus 239 ~~kC~LCLe~~---~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 239 TRKCSLCLENR---SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV 288 (293)
T ss_pred CCceEEEecCC---CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence 46999999998 789999999999999999999999999999998876543
No 11
>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=98.86 E-value=9.4e-10 Score=78.19 Aligned_cols=46 Identities=35% Similarity=0.840 Sum_probs=40.6
Q ss_pred cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
+..|.||++.. ..+..+||+|. ||..|+..|+.....||+||+++.
T Consensus 2 ~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 45799999998 77999999999 999999999999999999999874
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=98.82 E-value=1.5e-09 Score=73.22 Aligned_cols=38 Identities=42% Similarity=1.117 Sum_probs=32.8
Q ss_pred chhhhhhhccCCce-EEecCCCcccccchHHHHhcCCCCCCC
Q 036250 216 CAVCLEEFVMGNEA-KEMPCKHKFHGECIMPWLELQSSCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~-~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (347)
|+||++.+ .++ +.++|||+||..||.+|++.+..||+|
T Consensus 1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDEL---RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB----SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcc---cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999999 556 688999999999999999988899998
No 13
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.78 E-value=2.6e-09 Score=73.43 Aligned_cols=38 Identities=34% Similarity=0.937 Sum_probs=30.6
Q ss_pred chhhhhhhccCCceEEecCCCcccccchHHHHhcC----CCCCCC
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ----SSCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~~CP~C 256 (347)
|+||++.| .+++.|+|||.||..||..|++.. ..||+|
T Consensus 1 CpiC~~~~---~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF---KDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB----SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh---CCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999 899999999999999999999654 359987
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=3.8e-09 Score=71.60 Aligned_cols=43 Identities=44% Similarity=1.152 Sum_probs=35.8
Q ss_pred cchhhhhhhccCCceEEe-cCCCcccccchHHHHhc-CCCCCCCCccc
Q 036250 215 QCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLEL-QSSCPICRYQL 260 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l 260 (347)
.|+||++.+ ..+..+ +|+|.||..|+..|+.. ...||+||..+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999998 444444 49999999999999987 67899999764
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=98.74 E-value=4.7e-09 Score=77.52 Aligned_cols=49 Identities=22% Similarity=0.514 Sum_probs=43.7
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDL 265 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (347)
..|+||++.+ .+++.++|||+|+..||..|+..+.+||+|+..+...+.
T Consensus 2 ~~Cpi~~~~~---~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVM---KDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcC---CCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhc
Confidence 4799999999 678999999999999999999888899999998865543
No 16
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.65 E-value=8e-09 Score=107.41 Aligned_cols=50 Identities=44% Similarity=1.024 Sum_probs=44.0
Q ss_pred cccchhhhhhhccCCc--eEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNE--AKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
+..|+||+|.+..+.. +++|+|+|+||..|+..|+++.++||+||..+..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD 342 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence 5789999999965543 8999999999999999999999999999995533
No 17
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.61 E-value=1.1e-08 Score=90.11 Aligned_cols=50 Identities=26% Similarity=0.681 Sum_probs=42.3
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (347)
..|+|||+.+.. ..++-+.|||+||+.||+.-|.....||+|++.|..++
T Consensus 132 ~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSE-KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhh-ccccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 589999999953 22345679999999999999999999999999886654
No 18
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.60 E-value=1.8e-08 Score=100.18 Aligned_cols=51 Identities=31% Similarity=0.718 Sum_probs=45.1
Q ss_pred ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD 263 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (347)
+...+.|+||++.| ..++.++|+|.||..||..||.....||+||..+...
T Consensus 23 Le~~l~C~IC~d~~---~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFF---DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhh---hCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 34567999999999 6788899999999999999998888999999988654
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=98.59 E-value=1.8e-08 Score=68.31 Aligned_cols=38 Identities=42% Similarity=1.194 Sum_probs=33.2
Q ss_pred chhhhhhhccCCceE-EecCCCcccccchHHHHh--cCCCCCCC
Q 036250 216 CAVCLEEFVMGNEAK-EMPCKHKFHGECIMPWLE--LQSSCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~--~~~~CP~C 256 (347)
|+||++.+ ..+. .++|+|.||..||..|++ ....||+|
T Consensus 1 C~iC~~~~---~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF---EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBC---SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccc---cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999999 5566 889999999999999998 45579998
No 20
>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=98.57 E-value=2.6e-08 Score=65.07 Aligned_cols=38 Identities=45% Similarity=1.205 Sum_probs=34.0
Q ss_pred chhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCC
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~C 256 (347)
|+||++.. ..++.++|+|.||..|+..|+. ....||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 78999985 7889999999999999999998 56679987
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.55 E-value=3.1e-08 Score=68.56 Aligned_cols=44 Identities=27% Similarity=0.752 Sum_probs=38.5
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
.|.||++.|.....++.++|+|+||..||..+......||+||+
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 49999999965567899999999999999999866678999985
No 22
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.50 E-value=4.7e-08 Score=76.77 Aligned_cols=50 Identities=34% Similarity=0.788 Sum_probs=38.0
Q ss_pred ccccchhhhhhhcc--------CC-ce-EEecCCCcccccchHHHHhc---CCCCCCCCcccC
Q 036250 212 QDLQCAVCLEEFVM--------GN-EA-KEMPCKHKFHGECIMPWLEL---QSSCPICRYQLP 261 (347)
Q Consensus 212 ~~~~C~ICl~~~~~--------~~-~~-~~lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~ 261 (347)
++..|.||...|+. |+ .+ +.-.|+|.||..||.+||+. +..||+||++..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 46789999999852 22 23 33349999999999999975 467999999764
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.45 E-value=6e-08 Score=88.50 Aligned_cols=50 Identities=28% Similarity=0.669 Sum_probs=37.9
Q ss_pred ccccchhhhhhhccCC------ceEEecCCCcccccchHHHHhcC------CCCCCCCcccC
Q 036250 212 QDLQCAVCLEEFVMGN------EAKEMPCKHKFHGECIMPWLELQ------SSCPICRYQLP 261 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~------~~~~lpC~H~Fh~~Ci~~Wl~~~------~~CP~CR~~l~ 261 (347)
.+.+|+||++...... -....+|+|.||..||..|...+ .+||+||..+.
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 4679999999874321 12344699999999999999753 35999999764
No 24
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.40 E-value=8.5e-08 Score=91.94 Aligned_cols=53 Identities=36% Similarity=0.834 Sum_probs=47.1
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (347)
+.-+.|-||.++| ..+.++||+|.||..||...|..+..||.|+.++....+.
T Consensus 21 D~lLRC~IC~eyf---~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr 73 (442)
T KOG0287|consen 21 DDLLRCGICFEYF---NIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLR 73 (442)
T ss_pred HHHHHHhHHHHHh---cCceeccccchHHHHHHHHHhccCCCCCceecccchhhhh
Confidence 3456899999999 7889999999999999999999999999999988766544
No 25
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.40 E-value=7.8e-08 Score=96.79 Aligned_cols=55 Identities=36% Similarity=0.753 Sum_probs=46.1
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC-----CCCCCCCcccCCCCCcccC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ-----SSCPICRYQLPSDDLKVQG 269 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~CP~CR~~l~~~~~~~~~ 269 (347)
.+..|+|||+.. ..+..+.|||+||..||.++|... ..||+||..+..+++....
T Consensus 185 t~~~CPICL~~~---~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 185 TDMQCPICLEPP---SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred cCCcCCcccCCC---CcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence 367999999998 778888899999999999998653 4699999999887765443
No 26
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.32 E-value=1.4e-07 Score=88.03 Aligned_cols=50 Identities=32% Similarity=0.792 Sum_probs=43.2
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHH-HHhcCCC-CCCCCcccCCCC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMP-WLELQSS-CPICRYQLPSDD 264 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~-Wl~~~~~-CP~CR~~l~~~~ 264 (347)
.+..|.||++.. ..+..++|+|+||+.||.. |-..+.- ||+||+.+..++
T Consensus 214 ~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 214 ADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred cccceeeeeccc---CCcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 367899999999 8899999999999999999 8766654 999999876654
No 27
>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=98.28 E-value=3e-07 Score=70.60 Aligned_cols=51 Identities=25% Similarity=0.522 Sum_probs=41.0
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCCC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDDL 265 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~ 265 (347)
+.+.|+|+.+.| .+++++||||.|...||..||.. +.+||+|+..+...+.
T Consensus 3 ~~f~CpIt~~lM---~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELM---RDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB----SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred cccCCcCcCcHh---hCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence 456899999999 89999999999999999999988 7899999998876544
No 28
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=2.3e-07 Score=86.65 Aligned_cols=64 Identities=28% Similarity=0.656 Sum_probs=48.6
Q ss_pred cCCcccccccccchhhhhhhccCC-------ceEEecCCCcccccchHHHH--hcCCCCCCCCcccCCCCCccc
Q 036250 204 ALPTVAIDQDLQCAVCLEEFVMGN-------EAKEMPCKHKFHGECIMPWL--ELQSSCPICRYQLPSDDLKVQ 268 (347)
Q Consensus 204 ~lp~~~~~~~~~C~ICl~~~~~~~-------~~~~lpC~H~Fh~~Ci~~Wl--~~~~~CP~CR~~l~~~~~~~~ 268 (347)
.+|+..++ +..|+||-..+.... +..+|.|+|+||..||+-|- .++.+||.|+..+..+..-.+
T Consensus 216 glPtkhl~-d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsn 288 (328)
T KOG1734|consen 216 GLPTKHLS-DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSN 288 (328)
T ss_pred CCCCCCCC-cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccC
Confidence 34555443 457999999886544 67899999999999999997 467899999998865544333
No 29
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.25 E-value=4e-07 Score=62.88 Aligned_cols=38 Identities=32% Similarity=0.796 Sum_probs=22.6
Q ss_pred chhhhhhhcc-CCceEEecCCCcccccchHHHHhcC----CCCC
Q 036250 216 CAVCLEEFVM-GNEAKEMPCKHKFHGECIMPWLELQ----SSCP 254 (347)
Q Consensus 216 C~ICl~~~~~-~~~~~~lpC~H~Fh~~Ci~~Wl~~~----~~CP 254 (347)
|+||++ |.. ...++.|+|||+|+.+||.+|+... ..||
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 733 3348999999999999999999743 2476
No 30
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.18 E-value=7.4e-07 Score=68.63 Aligned_cols=49 Identities=31% Similarity=0.700 Sum_probs=36.7
Q ss_pred ccchhhhhhhc-----------cCC-ceEE-ecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 214 LQCAVCLEEFV-----------MGN-EAKE-MPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~-----------~~~-~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
..|+||...+. .+. .++. =-|.|.||..||.+||..++.||++|++...
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 46777777663 222 2222 2399999999999999999999999997643
No 31
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.09 E-value=1.2e-06 Score=82.58 Aligned_cols=48 Identities=31% Similarity=0.604 Sum_probs=43.0
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
.-+.|-||.+.| ..+..++|+|.||+-||...|..+.-||+||.+...
T Consensus 24 s~lrC~IC~~~i---~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 24 SMLRCRICDCRI---SIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred hHHHhhhhhhee---ecceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence 346899999999 778899999999999999999999999999987543
No 32
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.08 E-value=1.6e-06 Score=61.55 Aligned_cols=42 Identities=26% Similarity=0.777 Sum_probs=33.9
Q ss_pred cchhhhhhhccCCceEEecCC-----CcccccchHHHHhcC--CCCCCCC
Q 036250 215 QCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLELQ--SSCPICR 257 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR 257 (347)
.|-||++ ...+..+.++||. |.+|..||.+|+..+ .+||+|+
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 4889998 4445677889985 899999999999654 4799995
No 33
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=2.7e-06 Score=68.65 Aligned_cols=48 Identities=27% Similarity=0.601 Sum_probs=36.0
Q ss_pred cccchhhhhhhc-------------cCCc-eEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250 213 DLQCAVCLEEFV-------------MGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 213 ~~~C~ICl~~~~-------------~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
...|+||..-+. .++. +.-=-|.|.||..||.+||+.++.||+|.++-
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 357999887652 1121 23334999999999999999999999997753
No 34
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=1.9e-06 Score=79.89 Aligned_cols=46 Identities=39% Similarity=0.909 Sum_probs=39.5
Q ss_pred ccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
+.+...|+||++.| ..++.+||+|.||..||..++.....||.||.
T Consensus 10 ~~~~~~C~iC~~~~---~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYF---REPVLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHh---hcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 34567999999999 66699999999999999999885567999993
No 35
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.99 E-value=3e-06 Score=84.16 Aligned_cols=54 Identities=37% Similarity=0.897 Sum_probs=42.0
Q ss_pred CcccccccccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250 206 PTVAIDQDLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 206 p~~~~~~~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
+...+.+-.+|+|||+.+..... ++.+.|.|.||..|+.+|. ..+||+||+...
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 44445566799999999965432 3455599999999999994 578999999775
No 36
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=1.7e-06 Score=86.71 Aligned_cols=50 Identities=30% Similarity=0.947 Sum_probs=39.5
Q ss_pred cccchhhhhhhccC---C-----------ceEEecCCCcccccchHHHHh-cCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMG---N-----------EAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~---~-----------~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~ 262 (347)
...|+||+..+..- . .-..+||.|+||..|+.+|.+ .+-.||+||.+|+.
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 46899999987421 1 123559999999999999998 45589999999874
No 37
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.97 E-value=2.1e-06 Score=63.80 Aligned_cols=52 Identities=27% Similarity=0.737 Sum_probs=26.4
Q ss_pred cccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV 267 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~ 267 (347)
++.+.|++|.+.+ .+++.| .|.|+||+.||..-+. ..||+|+.+-...+.+.
T Consensus 5 e~lLrCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~ 57 (65)
T PF14835_consen 5 EELLRCSICFDIL---KEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQI 57 (65)
T ss_dssp HHTTS-SSS-S-----SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS---
T ss_pred HHhcCCcHHHHHh---cCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHh
Confidence 3456899999999 677655 4999999999988654 34999999887766554
No 38
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.96 E-value=3e-06 Score=90.22 Aligned_cols=53 Identities=30% Similarity=0.844 Sum_probs=40.1
Q ss_pred cccccccccchhhhhhhccCCceEEe------cCCCcccccchHHHHhc--CCCCCCCCcccC
Q 036250 207 TVAIDQDLQCAVCLEEFVMGNEAKEM------PCKHKFHGECIMPWLEL--QSSCPICRYQLP 261 (347)
Q Consensus 207 ~~~~~~~~~C~ICl~~~~~~~~~~~l------pC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~ 261 (347)
..++..-.+|+||...+..- -+.+ .|+|.||..||.+|+.. +++||+||.+++
T Consensus 1463 ~~~fsG~eECaICYsvL~~v--dr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1463 DEKFSGHEECAICYSVLDMV--DRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hhhcCCcchhhHHHHHHHHH--hccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 34555667999999988511 1233 29999999999999965 467999998775
No 39
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=1.2e-06 Score=66.93 Aligned_cols=49 Identities=37% Similarity=0.862 Sum_probs=36.2
Q ss_pred cccchhhhhhhcc--------C-CceEEec-CCCcccccchHHHHhc---CCCCCCCCcccC
Q 036250 213 DLQCAVCLEEFVM--------G-NEAKEMP-CKHKFHGECIMPWLEL---QSSCPICRYQLP 261 (347)
Q Consensus 213 ~~~C~ICl~~~~~--------~-~~~~~lp-C~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~ 261 (347)
+..|-||.-.|.. | +.+.++- |.|.||..||.+||.. +..||+||++..
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 4578899888842 2 2333333 9999999999999964 346999998764
No 40
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.79 E-value=4.3e-06 Score=63.76 Aligned_cols=50 Identities=26% Similarity=0.714 Sum_probs=23.4
Q ss_pred cccchhhhhhhc-cCCceEEe----cCCCcccccchHHHHhc----C-------CCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFV-MGNEAKEM----PCKHKFHGECIMPWLEL----Q-------SSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~-~~~~~~~l----pC~H~Fh~~Ci~~Wl~~----~-------~~CP~CR~~l~~ 262 (347)
+.+|.||+..+. .+..+.++ .|++.||..||..||.. + ..||.|+.+|..
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 458999999875 33332222 38999999999999953 1 139999998753
No 41
>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=97.77 E-value=1.2e-05 Score=77.40 Aligned_cols=54 Identities=20% Similarity=0.433 Sum_probs=39.2
Q ss_pred cccchhhhhhhccCCce--EEecCCCcccccchHHHH-hcCCCCCCCCcccCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEA--KEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~--~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~ 266 (347)
+..|+||+..-...... ...+|||.||..||...+ .....||.|+..+....+.
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 35799999953333332 233799999999999966 4456899999988776543
No 42
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=1.5e-05 Score=77.48 Aligned_cols=47 Identities=28% Similarity=0.737 Sum_probs=41.5
Q ss_pred cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
..+|.||+.+- .+..+|||.|. .|..|.+.---+++.||+||+++..
T Consensus 290 gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 290 GKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred CCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 46899999998 78899999999 8999988766678999999998854
No 43
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=7.8e-06 Score=79.17 Aligned_cols=51 Identities=31% Similarity=0.712 Sum_probs=40.3
Q ss_pred ccccccchhhhhhhccCCceEEec-CCCcccccchHHHHhc-CCCCCCCCcccCCC
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLEL-QSSCPICRYQLPSD 263 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~ 263 (347)
+..+..|+|||+.+ ...+..+ |.|.||..||..-+.. .+.||.||+.+.+.
T Consensus 40 ~~~~v~c~icl~ll---k~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 40 FDIQVICPICLSLL---KKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred hhhhhccHHHHHHH---HhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 34467899999999 4344444 9999999999998855 56899999988654
No 44
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.64 E-value=1.6e-05 Score=75.51 Aligned_cols=48 Identities=27% Similarity=0.580 Sum_probs=41.2
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhc-CCCCCCCCcccCCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQLPSDD 264 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~ 264 (347)
.+|+||+... ..++.|+|+|.||..||+--..+ ..+|++||+++++.-
T Consensus 8 ~eC~IC~nt~---n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 8 KECLICYNTG---NCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred CcceeeeccC---CcCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 4799999998 78899999999999999877654 456999999997753
No 45
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.52 E-value=2.2e-05 Score=74.57 Aligned_cols=91 Identities=19% Similarity=0.448 Sum_probs=58.1
Q ss_pred chHHHHHHHHhcCCCCCCCCcchHHHHHcCCcc---cccccccchhhhhhhccCCceEEecCCCcccccchHHHHh----
Q 036250 176 GLDLLLQHLLENDPNRYGSLPAQKEVVKALPTV---AIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE---- 248 (347)
Q Consensus 176 ~ld~l~~~l~~~~~~~~~~~p~~~~~i~~lp~~---~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~---- 248 (347)
.|..|.+++...-....| .|.--+.|+..... .-.....|.|||.-|..+....+++|-|+||..|+-.+|.
T Consensus 76 ~~~~i~~~~~~iikq~~g-~pii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~ 154 (368)
T KOG4445|consen 76 EFREIQRQIQEIIKQNSG-MPIICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLT 154 (368)
T ss_pred HHHHHHHHHHHHHHhcCC-CchhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHH
Confidence 455666665443322344 33334444432211 1123468999999999888899999999999999955542
Q ss_pred --------------c-----CCCCCCCCcccCCCCCcc
Q 036250 249 --------------L-----QSSCPICRYQLPSDDLKV 267 (347)
Q Consensus 249 --------------~-----~~~CP~CR~~l~~~~~~~ 267 (347)
. ...||+||..|..+....
T Consensus 155 ~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~sl 192 (368)
T KOG4445|consen 155 GLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENSL 192 (368)
T ss_pred HHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccce
Confidence 1 124999999886654443
No 46
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.42 E-value=4.1e-05 Score=80.52 Aligned_cols=54 Identities=26% Similarity=0.485 Sum_probs=46.0
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (347)
...|++|+..+..+......+|.|+||..||..|-...++||+||..+......
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~ 176 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVL 176 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeeee
Confidence 357999999998766667778999999999999999999999999987655433
No 47
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.41 E-value=0.00011 Score=72.38 Aligned_cols=50 Identities=26% Similarity=0.776 Sum_probs=42.5
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhc--CCCCCCCCcccCCCCCcc
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL--QSSCPICRYQLPSDDLKV 267 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~~ 267 (347)
.|.||-+.- .++++-||||+.|..|+-.|-.. .++||.||.++...+..+
T Consensus 371 LCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi 422 (563)
T KOG1785|consen 371 LCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI 422 (563)
T ss_pred HHHHhhccC---CCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence 699999876 78899999999999999999843 578999999997766543
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=7.6e-05 Score=73.14 Aligned_cols=49 Identities=31% Similarity=0.838 Sum_probs=36.1
Q ss_pred ccchhhhhhhccCCceEEec-CCCcccccchHHHHhcC---CCCCCCCcccCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQ---SSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~ 262 (347)
..|.||-+.+-...++.-+. |||+||..|+.+|++.. ..||+|+-.++.
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~ 57 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQE 57 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccc
Confidence 37999966664444444444 99999999999999864 369999944433
No 49
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=3.9e-05 Score=55.09 Aligned_cols=45 Identities=27% Similarity=0.621 Sum_probs=35.8
Q ss_pred ccchhhhhhhccCCceEEecCCCc-ccccchHHHH-hcCCCCCCCCcccC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWL-ELQSSCPICRYQLP 261 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl-~~~~~CP~CR~~l~ 261 (347)
.+|.||++.- .+-+.-.|+|. .|..|-..-+ ..+..||+||.++.
T Consensus 8 dECTICye~p---vdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHP---VDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCc---chHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 5899999886 45556679998 7888876555 47889999999874
No 50
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.14 E-value=8.6e-05 Score=78.34 Aligned_cols=51 Identities=31% Similarity=0.705 Sum_probs=42.8
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHh-cCCCCCCCCcccCCCCC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE-LQSSCPICRYQLPSDDL 265 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~~ 265 (347)
+-+.|++|-..+ .+++++.|+|+||..||.+.+. ++..||.|...+...|.
T Consensus 642 ~~LkCs~Cn~R~---Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 642 ELLKCSVCNTRW---KDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred hceeCCCccCch---hhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 457999999888 6777888999999999999996 45789999998866554
No 51
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00021 Score=71.47 Aligned_cols=49 Identities=31% Similarity=0.760 Sum_probs=43.7
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
..+..|.||+..+ -.++.+||+|.||..||.+-+.....||+||..+..
T Consensus 82 ~sef~c~vc~~~l---~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL---YPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc---CCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence 3467999999999 778899999999999999988877889999999875
No 52
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.05 E-value=0.00032 Score=68.93 Aligned_cols=54 Identities=28% Similarity=0.712 Sum_probs=38.9
Q ss_pred ccccccccchhhhhhhccCC----ceEEec-CCCcccccchHHHH--hc-----CCCCCCCCcccC
Q 036250 208 VAIDQDLQCAVCLEEFVMGN----EAKEMP-CKHKFHGECIMPWL--EL-----QSSCPICRYQLP 261 (347)
Q Consensus 208 ~~~~~~~~C~ICl~~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl--~~-----~~~CP~CR~~l~ 261 (347)
.....+..|.||++...... .-.+|| |.|.||..||..|- .+ ...||.||....
T Consensus 156 ~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 156 LQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 33356779999999985322 012335 99999999999998 33 357999998653
No 53
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.91 E-value=0.00036 Score=70.03 Aligned_cols=52 Identities=27% Similarity=0.844 Sum_probs=44.6
Q ss_pred ccccccchhhhhhhccCCceEE-ecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKE-MPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (347)
+++++.|+||...+ .++.. ..|+|.||..||..|+..+..||.|+..+....
T Consensus 18 ~~~~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 18 LDENLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE 70 (391)
T ss_pred CcccccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence 45668999999999 66666 589999999999999999999999988775543
No 54
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.76 E-value=0.00033 Score=67.61 Aligned_cols=50 Identities=26% Similarity=0.679 Sum_probs=42.1
Q ss_pred cccccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPSD 263 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (347)
.....|.+|...| .++..+. |-|.||..||...|+...+||.|...+-..
T Consensus 13 n~~itC~LC~GYl---iDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 13 NPHITCRLCGGYL---IDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred ccceehhhcccee---ecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 3456899999999 5666665 999999999999999999999998877544
No 55
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.00073 Score=66.82 Aligned_cols=48 Identities=27% Similarity=0.826 Sum_probs=36.6
Q ss_pred cccchhhhhhhccC--CceEEecCCCcccccchHHHHhc--CCCCCCCCccc
Q 036250 213 DLQCAVCLEEFVMG--NEAKEMPCKHKFHGECIMPWLEL--QSSCPICRYQL 260 (347)
Q Consensus 213 ~~~C~ICl~~~~~~--~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l 260 (347)
..+|+||++.+.-. ...+.+.|+|.|...||.+||.+ ...||.|...-
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 35899999998532 24556679999999999999953 23599997643
No 56
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.46 E-value=0.0015 Score=47.83 Aligned_cols=40 Identities=28% Similarity=0.806 Sum_probs=27.9
Q ss_pred cccchhhhhhhccCCceEEe-cCCCcccccchHHHHhcC--CCCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLELQ--SSCPI 255 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~--~~CP~ 255 (347)
...|+|.+..| .++++- .|+|+|-...|..||..+ ..||+
T Consensus 11 ~~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 46899999999 677665 699999999999999443 35998
No 57
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.27 E-value=0.0012 Score=59.69 Aligned_cols=44 Identities=18% Similarity=0.594 Sum_probs=39.6
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
..|.||..+| ..++...|+|.||..|...-......|-+|-+..
T Consensus 197 F~C~iCKkdy---~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 197 FLCGICKKDY---ESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred eeehhchhhc---cchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 5799999999 7888999999999999999888888999997654
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.23 E-value=0.0014 Score=64.55 Aligned_cols=48 Identities=35% Similarity=0.767 Sum_probs=38.9
Q ss_pred cccchhhhhhhccC-CceEEecCCCcccccchHHHHhcC--CCCCCCCccc
Q 036250 213 DLQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQ--SSCPICRYQL 260 (347)
Q Consensus 213 ~~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l 260 (347)
++.|..|-+.+... +..--|||.|+||..|+...|+++ .+||.||+-.
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 46899999998543 456778999999999999999765 4799999533
No 59
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.96 E-value=0.0036 Score=57.59 Aligned_cols=52 Identities=21% Similarity=0.530 Sum_probs=40.9
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--C------CCCCCCcccCCCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--S------SCPICRYQLPSDDL 265 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~------~CP~CR~~l~~~~~ 265 (347)
..-|..|...+..|+.+ +|-|-|+||+.|+..|-..- + .||.|..+|.....
T Consensus 50 ~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~N 109 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPIN 109 (299)
T ss_pred CCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcc
Confidence 34799999999887755 66699999999999997542 2 39999998866533
No 60
>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=95.82 E-value=0.0037 Score=53.30 Aligned_cols=35 Identities=14% Similarity=0.485 Sum_probs=29.9
Q ss_pred cccchhhhhhhccCCceEEecCC------CcccccchHHHH
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCK------HKFHGECIMPWL 247 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~------H~Fh~~Ci~~Wl 247 (347)
..+|.||++.+....-++.++|+ |.||..|+.+|-
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 45899999999775567888886 899999999994
No 61
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.0026 Score=55.75 Aligned_cols=28 Identities=29% Similarity=0.809 Sum_probs=26.2
Q ss_pred cccchhhhhhhccCCceEEecCCCcccc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHG 240 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~ 240 (347)
.-+|.||||+++.|+++.+|||-.+||+
T Consensus 177 kGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 177 KGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred CCcEEEEhhhccCCCceeccceEEEeec
Confidence 4699999999999999999999999996
No 62
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.0045 Score=60.56 Aligned_cols=45 Identities=33% Similarity=0.672 Sum_probs=33.9
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccC
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
.....|.||++.. ...+.+||||+-| |..-.. .-..||+||..+.
T Consensus 303 ~~p~lcVVcl~e~---~~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEP---KSAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCc---cceeeecCCcEEE--chHHHh-hCCCCchhHHHHH
Confidence 3456899999999 6689999999866 664432 2345999998764
No 63
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.50 E-value=0.0036 Score=63.85 Aligned_cols=50 Identities=30% Similarity=0.745 Sum_probs=41.5
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhc-----CCCCCCCCcccCCCC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL-----QSSCPICRYQLPSDD 264 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-----~~~CP~CR~~l~~~~ 264 (347)
+..+|-+|-+.- ++.+...|.|.||..||..++.. .-+||+|...|..+.
T Consensus 535 ~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 535 GEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred CceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 346899999998 77889999999999999888853 347999999887663
No 64
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.47 E-value=0.0041 Score=59.37 Aligned_cols=46 Identities=22% Similarity=0.515 Sum_probs=40.8
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
..|-||...| ..+++..|+|.||..|...-+.....|.+|-+....
T Consensus 242 f~c~icr~~f---~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYF---YRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccc---ccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 4699999999 788999999999999999988888999999876643
No 65
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.36 E-value=0.0074 Score=57.68 Aligned_cols=46 Identities=30% Similarity=0.685 Sum_probs=37.6
Q ss_pred ccchhhhhhhccCCceEEec-CCCcccccchHHHH-hcCCCCCCCCc-ccCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWL-ELQSSCPICRY-QLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl-~~~~~CP~CR~-~l~~ 262 (347)
+.|+.|...+ ..+.++| |+|.||..||..-| +....||.|.. .+..
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvll 323 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLL 323 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCcccccchh
Confidence 6899999998 7788887 89999999998776 56678999944 4433
No 66
>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=95.35 E-value=0.0062 Score=49.16 Aligned_cols=37 Identities=30% Similarity=0.587 Sum_probs=30.6
Q ss_pred cccccccccchhhhhhhccCCceEEecCCCcccccchH
Q 036250 207 TVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIM 244 (347)
Q Consensus 207 ~~~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~ 244 (347)
.+.+++...|+||...+.. ......||+|+||..|+.
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 3456677889999999965 567788999999999974
No 67
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.16 E-value=0.009 Score=66.90 Aligned_cols=50 Identities=34% Similarity=0.717 Sum_probs=40.4
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC----------CCCCCCcccC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS----------SCPICRYQLP 261 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----------~CP~CR~~l~ 261 (347)
.+..|-||..+-......++|.|+|+||..|...-|+++- +||+|+.++.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 3678999998876666788999999999999977766532 4999998774
No 68
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=95.14 E-value=0.014 Score=48.64 Aligned_cols=36 Identities=19% Similarity=0.518 Sum_probs=30.2
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecCCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSS 42 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~~ 42 (347)
....||..|..++.+... ++.||.|+|..+.-+...
T Consensus 68 p~~~~C~~C~~~~~~e~~-~~~CP~C~s~~~~i~~G~ 103 (115)
T COG0375 68 PAECWCLDCGQEVELEEL-DYRCPKCGSINLRIIGGD 103 (115)
T ss_pred ccEEEeccCCCeecchhh-eeECCCCCCCceEEecCC
Confidence 467899999999987766 688999999999877654
No 69
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.14 E-value=0.013 Score=41.07 Aligned_cols=40 Identities=30% Similarity=0.802 Sum_probs=26.7
Q ss_pred chhhhhhhccCCceEEecCC--C---cccccchHHHHhc--CCCCCCC
Q 036250 216 CAVCLEEFVMGNEAKEMPCK--H---KFHGECIMPWLEL--QSSCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~C 256 (347)
|-||++.-.... +.+.||. - ..|..||..|+.. ..+|++|
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 678998875533 5677864 3 7899999999964 4569887
No 70
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.11 E-value=0.01 Score=57.97 Aligned_cols=49 Identities=24% Similarity=0.466 Sum_probs=43.3
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
.++..|+||...- ..++..||+|.-|+.||.+-|.+.+.|=.|+..+..
T Consensus 420 sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 420 SEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred cccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 3567899998876 778899999999999999999999999999998764
No 71
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.09 E-value=0.012 Score=55.67 Aligned_cols=47 Identities=26% Similarity=0.522 Sum_probs=36.8
Q ss_pred ccccchhhhhhhccCCceEEe-cCCCcccccchHHHHhc--CCCCCCCCcccC
Q 036250 212 QDLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWLEL--QSSCPICRYQLP 261 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~ 261 (347)
.+.+|++|-+.- .-+.++ +|+|+||..||..-+.. ..+||.|-.++.
T Consensus 238 ~~~~C~~Cg~~P---tiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPP---TIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCC---CCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 457999999887 445554 49999999999887653 468999987665
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.89 E-value=0.0096 Score=59.22 Aligned_cols=46 Identities=28% Similarity=0.666 Sum_probs=37.1
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC--------CCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS--------SCPICRY 258 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--------~CP~CR~ 258 (347)
...|.||+++..-....+.+||+|+||..|+..++..+- .||-+..
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 358999999986557899999999999999999985421 3776654
No 73
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.39 E-value=0.011 Score=56.35 Aligned_cols=42 Identities=26% Similarity=0.632 Sum_probs=33.0
Q ss_pred cccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
...|+||++.- .+-+.|+|||. -|..|-.. -+.||+||+.+.
T Consensus 300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence 35799999998 78899999997 56667533 247999998763
No 74
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.23 E-value=0.017 Score=40.73 Aligned_cols=44 Identities=30% Similarity=0.589 Sum_probs=21.8
Q ss_pred chhhhhhhccCCceEEec--CCCcccccchHHHHh-cCCCCCCCCccc
Q 036250 216 CAVCLEEFVMGNEAKEMP--CKHKFHGECIMPWLE-LQSSCPICRYQL 260 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l 260 (347)
|++|.+++.. .....+| |++.+|..|...-++ ....||-||.+.
T Consensus 1 cp~C~e~~d~-~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDE-TDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--C-CCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCccccccc-CCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899999833 3334555 889999999888775 467899999864
No 75
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=94.14 E-value=0.037 Score=53.65 Aligned_cols=47 Identities=21% Similarity=0.480 Sum_probs=37.9
Q ss_pred cccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
...|+||+... ..+..+. -|-+||+.||...+..++.||+=-.+...
T Consensus 300 ~~~CpvClk~r---~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v 347 (357)
T KOG0826|consen 300 REVCPVCLKKR---QNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASV 347 (357)
T ss_pred cccChhHHhcc---CCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchH
Confidence 46899999998 4444444 69999999999999999999997666543
No 76
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.74 E-value=0.033 Score=40.34 Aligned_cols=45 Identities=24% Similarity=0.531 Sum_probs=32.9
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (347)
.|-.|...- .+...+||+|+.+..|..-+ +-+.||+|-+++...+
T Consensus 9 ~~~~~~~~~---~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 9 PCVFCGFVG---TKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD 53 (55)
T ss_pred eEEEccccc---cccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence 344454443 56789999999999997553 6678999988886543
No 77
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.42 E-value=0.027 Score=60.46 Aligned_cols=48 Identities=27% Similarity=0.668 Sum_probs=33.9
Q ss_pred ccccchhhhhhhccCCceE-EecCCCcccccchHHHHhcCC-------CCCCCCcc
Q 036250 212 QDLQCAVCLEEFVMGNEAK-EMPCKHKFHGECIMPWLELQS-------SCPICRYQ 259 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~-------~CP~CR~~ 259 (347)
...+|.||++.+.....+- --.|-|+||..||..|-.... .||.|...
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence 3468999999995422211 113889999999999985421 39999843
No 78
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.41 E-value=0.0069 Score=59.78 Aligned_cols=50 Identities=24% Similarity=0.618 Sum_probs=42.6
Q ss_pred ccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcccCCC
Q 036250 214 LQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSD 263 (347)
Q Consensus 214 ~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (347)
..|+||.+.+... +....+-|+|.+|..||.+||.....||.|+.+|+..
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 4799999988644 4567778999999999999999999999999988654
No 79
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.39 E-value=0.027 Score=52.44 Aligned_cols=47 Identities=19% Similarity=0.492 Sum_probs=34.3
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (347)
.|..|..--. +.....+.|.|+||..|...- ....||+|++.+....
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i~ 51 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRIIQ 51 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhcccC--Cccccccccceeeeee
Confidence 5777765544 566778889999999998552 2228999999875543
No 80
>PHA02862 5L protein; Provisional
Probab=93.33 E-value=0.029 Score=48.38 Aligned_cols=45 Identities=18% Similarity=0.548 Sum_probs=33.6
Q ss_pred ccchhhhhhhccCCceEEecCC-----CcccccchHHHHhc--CCCCCCCCcccCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLEL--QSSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~ 262 (347)
..|=||++.-+ +. .-||. ..-|..|+..|+.. +..|++|+.+..-
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 46999999853 22 46764 46899999999954 4569999998743
No 81
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.96 E-value=0.038 Score=49.28 Aligned_cols=50 Identities=24% Similarity=0.673 Sum_probs=35.9
Q ss_pred ccchhhhhhhccCCceE----EecCCCcccccchHHHHhc----CC-------CCCCCCcccCCC
Q 036250 214 LQCAVCLEEFVMGNEAK----EMPCKHKFHGECIMPWLEL----QS-------SCPICRYQLPSD 263 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~----~lpC~H~Fh~~Ci~~Wl~~----~~-------~CP~CR~~l~~~ 263 (347)
..|-||...-..|..+- -..|+..||.-|+..||.. +. .||+|-.++..+
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 46888877665554332 3359999999999999964 11 399999887654
No 82
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=92.89 E-value=0.076 Score=59.53 Aligned_cols=82 Identities=24% Similarity=0.462 Sum_probs=51.5
Q ss_pred cCCchHHHHHHHHhcCCCCCCCCcchHHHHHcCCcccccccccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCC
Q 036250 173 VGPGLDLLLQHLLENDPNRYGSLPAQKEVVKALPTVAIDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSS 252 (347)
Q Consensus 173 ~g~~ld~l~~~l~~~~~~~~~~~p~~~~~i~~lp~~~~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~ 252 (347)
.-+|+-.++..|.+.........+-.+..+.- ...+.....|.||++.+.. .-.+.-|+|.+|..|+..|+..+..
T Consensus 1115 s~~G~~r~lk~l~e~~~~~~~~i~~~es~~~y--~~~~~~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~ 1190 (1394)
T KOG0298|consen 1115 SIPGLLRYLKGLKESKADTPCKIAQTESDVRY--LMNLSGHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSR 1190 (1394)
T ss_pred ccchHHHHHHHHHHHhccCccccCCccchHHH--HHHhhcccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhcc
Confidence 33566666666665443322222111111111 1122234589999999952 3345569999999999999999999
Q ss_pred CCCCCc
Q 036250 253 CPICRY 258 (347)
Q Consensus 253 CP~CR~ 258 (347)
||.|+.
T Consensus 1191 ~~~~ks 1196 (1394)
T KOG0298|consen 1191 CPICKS 1196 (1394)
T ss_pred Ccchhh
Confidence 999984
No 83
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.71 E-value=0.084 Score=49.41 Aligned_cols=54 Identities=19% Similarity=0.247 Sum_probs=45.1
Q ss_pred ccchhhhhhhccCC-ceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250 214 LQCAVCLEEFVMGN-EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV 267 (347)
Q Consensus 214 ~~C~ICl~~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~ 267 (347)
..|+||.+.+.... .++.-||+|+|+..|+.+.+..-..||+|-.++...+...
T Consensus 222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~ 276 (303)
T KOG3039|consen 222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIG 276 (303)
T ss_pred eecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEe
Confidence 57999999996544 3555579999999999999988899999999998876554
No 84
>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=92.35 E-value=0.033 Score=38.38 Aligned_cols=41 Identities=27% Similarity=0.799 Sum_probs=22.7
Q ss_pred chhhhhhhccCCceEEecCCCcccccchHHHHhcCC--CCCCC
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS--SCPIC 256 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~C 256 (347)
|.+|.+.+..|..-....|.=.+|..|+..++.... .||.|
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 678888885443222223888999999999997665 69987
No 85
>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=92.19 E-value=0.12 Score=51.16 Aligned_cols=31 Identities=29% Similarity=0.763 Sum_probs=23.5
Q ss_pred CCCcccccchHHHHhcC-------------CCCCCCCcccCCCC
Q 036250 234 CKHKFHGECIMPWLELQ-------------SSCPICRYQLPSDD 264 (347)
Q Consensus 234 C~H~Fh~~Ci~~Wl~~~-------------~~CP~CR~~l~~~~ 264 (347)
|...+|.+|+-+|+..+ -.||+||+.+..-|
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence 56778999998888442 35999999876554
No 86
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.07 E-value=0.07 Score=52.16 Aligned_cols=47 Identities=26% Similarity=0.753 Sum_probs=38.5
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHH--HHhcCCCCCCCCccc
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMP--WLELQSSCPICRYQL 260 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~--Wl~~~~~CP~CR~~l 260 (347)
++...|.||.+.+ .-..++||+|..|-.|... -|.....||+||.+-
T Consensus 59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 3456899999998 6678999999999999854 456788999999864
No 87
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=92.01 E-value=0.084 Score=50.51 Aligned_cols=45 Identities=27% Similarity=0.696 Sum_probs=38.0
Q ss_pred ccchhhhhhhccCC-ceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 214 LQCAVCLEEFVMGN-EAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 214 ~~C~ICl~~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
..|+||.+.+.... .+..++|+|..|..|+......+-+||+|.+
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 45999999986554 5778899999999999888866788999988
No 88
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=91.56 E-value=0.17 Score=42.24 Aligned_cols=35 Identities=23% Similarity=0.458 Sum_probs=27.3
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS 41 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~ 41 (347)
..+.||+.|...+.+... .+.||.|++..++-+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID-LYRCPKCHGIMLQVRAG 102 (115)
T ss_pred CcEEEcccCCCEEecCCc-CccCcCCcCCCcEEecC
Confidence 578999999988875433 57899999987665543
No 89
>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=91.32 E-value=0.11 Score=31.39 Aligned_cols=22 Identities=36% Similarity=0.919 Sum_probs=18.7
Q ss_pred eecCCceeeecC-CCCccCCCCC
Q 036250 11 CYICSRMVNPRM-EAGIKCPFCE 32 (347)
Q Consensus 11 Ch~C~~~V~p~~-~~e~~CP~C~ 32 (347)
|..|.+.|.|.- ...++||.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 789999998875 5579999996
No 90
>PHA03096 p28-like protein; Provisional
Probab=91.22 E-value=0.088 Score=50.73 Aligned_cols=45 Identities=27% Similarity=0.455 Sum_probs=31.2
Q ss_pred ccchhhhhhhccCC----ceEEec-CCCcccccchHHHHhcC---CCCCCCCc
Q 036250 214 LQCAVCLEEFVMGN----EAKEMP-CKHKFHGECIMPWLELQ---SSCPICRY 258 (347)
Q Consensus 214 ~~C~ICl~~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~ 258 (347)
..|.||++...... .--.|+ |.|.||..||..|-... .+||.||.
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 57999999885421 223455 99999999999998432 23555543
No 91
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=90.91 E-value=0.1 Score=45.79 Aligned_cols=47 Identities=28% Similarity=0.662 Sum_probs=34.0
Q ss_pred cccchhhhhhhccCCceEEecCC--C---cccccchHHHHhcC--CCCCCCCcccCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCK--H---KFHGECIMPWLELQ--SSCPICRYQLPSD 263 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~ 263 (347)
+..|=||.+.-. .-.-||. . .-|.+|+..|+... .+|++|+.+....
T Consensus 8 ~~~CRIC~~~~~----~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 8 DKCCWICKDEYD----VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCeeEecCCCCC----CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 458999998852 2235754 4 56999999999654 4699998876443
No 92
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.90 E-value=0.099 Score=50.16 Aligned_cols=47 Identities=23% Similarity=0.615 Sum_probs=38.3
Q ss_pred ccchhhhhhhccC---CceEEecCCCcccccchHHHHhc-CCCCCCCCccc
Q 036250 214 LQCAVCLEEFVMG---NEAKEMPCKHKFHGECIMPWLEL-QSSCPICRYQL 260 (347)
Q Consensus 214 ~~C~ICl~~~~~~---~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l 260 (347)
..|-||-++|..+ ..++.|.|+|.||..|+.+-+.. ...||.||.+.
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 4799999999765 24778889999999999877754 34699999985
No 93
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=90.43 E-value=0.21 Score=41.59 Aligned_cols=36 Identities=19% Similarity=0.585 Sum_probs=26.3
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS 41 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~ 41 (347)
..++||..|...+......-..||.|+|.-++=+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGDMLRIVAD 103 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCCCcEEccC
Confidence 678999999988864433126699999887665543
No 94
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=90.25 E-value=0.082 Score=56.69 Aligned_cols=50 Identities=26% Similarity=0.625 Sum_probs=41.2
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcC--CCCCCCCcccCCCCCcc
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ--SSCPICRYQLPSDDLKV 267 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~~~~ 267 (347)
..|.||++ . +.+...+|+|.||..|+..-+... ..||+||..+..+....
T Consensus 455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence 78999999 4 788999999999999999988653 25999999886665443
No 95
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=90.22 E-value=0.22 Score=41.36 Aligned_cols=34 Identities=24% Similarity=0.657 Sum_probs=26.1
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMS 40 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~ 40 (347)
..++||..|.....+... .+.||.|++.-++-+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH-DAQCPHCHGERLRVDT 101 (113)
T ss_pred CcEEEcccCCCEEecCCc-CccCcCCCCCCcEEcc
Confidence 678999999988865432 5779999987666554
No 96
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.96 E-value=0.12 Score=55.84 Aligned_cols=43 Identities=23% Similarity=0.616 Sum_probs=34.0
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
...|.+|--.++ -..+..-|+|.||.+|+. .....||.|+.++
T Consensus 840 ~skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLD--LPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCccc--cceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 358999998884 345666799999999997 4566899998844
No 97
>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=89.67 E-value=0.22 Score=43.71 Aligned_cols=32 Identities=25% Similarity=0.649 Sum_probs=22.9
Q ss_pred cccchhhhhhhccCCceEEecCC------------C-cccccchHHHH
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCK------------H-KFHGECIMPWL 247 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~------------H-~Fh~~Ci~~Wl 247 (347)
+..|+||+|.- -.++.|-|. . .-|..||+++-
T Consensus 2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 46899999987 566676553 2 24788998774
No 98
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.50 E-value=0.3 Score=40.87 Aligned_cols=36 Identities=19% Similarity=0.214 Sum_probs=26.1
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS 41 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~ 41 (347)
..++||..|.....+.-.....||.|+|-.++=+..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSKNVIITQG 104 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCCceEEecC
Confidence 678999999988764422234599999988775543
No 99
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.37 E-value=0.22 Score=47.26 Aligned_cols=53 Identities=21% Similarity=0.447 Sum_probs=40.2
Q ss_pred cccchhhhhhhccCCc-eEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (347)
...|+|...+|..... +...||||+|...+|..-- ....||+|-.++...+..
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 3589999999944334 4455899999999998862 355799999998766544
No 100
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=89.35 E-value=0.12 Score=49.79 Aligned_cols=42 Identities=29% Similarity=0.661 Sum_probs=29.2
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
.|.-|--.+. .--+.+||+|+||.+|... ..-+.||+|-..|
T Consensus 92 fCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 5666655543 3347889999999999743 3456799996654
No 101
>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=89.01 E-value=0.2 Score=41.62 Aligned_cols=34 Identities=26% Similarity=0.457 Sum_probs=23.9
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMS 40 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~ 40 (347)
..++||..|.....+... .+.||.|++..++=+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEF-DFSCPRCGSPDVEIIS 101 (113)
T ss_dssp --EEEETTTS-EEECHHC-CHH-SSSSSS-EEEEE
T ss_pred CCcEECCCCCCEEecCCC-CCCCcCCcCCCcEEcc
Confidence 578999999999987655 5889999999876544
No 102
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=88.22 E-value=0.15 Score=43.46 Aligned_cols=47 Identities=26% Similarity=0.687 Sum_probs=36.0
Q ss_pred ccchhhhhhhccCCceEEe-c---CCCcccccchHHHHh---cCCCCCCCCcccCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEM-P---CKHKFHGECIMPWLE---LQSSCPICRYQLPSD 263 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~l-p---C~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~ 263 (347)
-+|.||.|... +.+-| | ||-..|..|....|+ .+..||+|+..+.+.
T Consensus 81 YeCnIC~etS~---ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKETSA---EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccccc---hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 58999999983 33333 3 999999999877664 467899999987654
No 103
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=88.12 E-value=0.23 Score=36.86 Aligned_cols=28 Identities=29% Similarity=0.624 Sum_probs=21.1
Q ss_pred eeecCCceeeecCCCCccCCCCCCC-ceEecC
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCETG-FVEQMS 40 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~sG-FiEE~~ 40 (347)
=|+.|.+.+. ++.-+||.|+|- |.||-.
T Consensus 6 AC~~Ck~l~~---~d~e~CP~Cgs~~~te~W~ 34 (64)
T COG2093 6 ACKNCKRLTP---EDTEICPVCGSTDLTEEWF 34 (64)
T ss_pred HHhhccccCC---CCCccCCCCCCcccchhhc
Confidence 3999999875 224579999996 877754
No 104
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.86 E-value=0.34 Score=48.28 Aligned_cols=48 Identities=19% Similarity=0.323 Sum_probs=39.8
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhcC---CCCCCCCcc
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ---SSCPICRYQ 259 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~ 259 (347)
....|+|=.+.-.....|..|.|||+...+-|.+..... ..||+|-.+
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 346899999988877889999999999999998877553 469999543
No 105
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=87.31 E-value=0.23 Score=49.96 Aligned_cols=36 Identities=28% Similarity=0.658 Sum_probs=31.2
Q ss_pred cccccchhhhhhhccCCceEEecCCCcccccchHHHHhc
Q 036250 211 DQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL 249 (347)
Q Consensus 211 ~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~ 249 (347)
++++.|+||-..| .++++|||+|..|..|...-+..
T Consensus 2 eeelkc~vc~~f~---~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFY---REPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhc---cCceEeecccHHHHHHHHhhccc
Confidence 4678999999999 88999999999999998766543
No 106
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.91 E-value=0.43 Score=33.85 Aligned_cols=29 Identities=34% Similarity=0.864 Sum_probs=22.9
Q ss_pred CCcEeeecCCceee-ecCCCCccCCCCCCC
Q 036250 6 VGSYWCYICSRMVN-PRMEAGIKCPFCETG 34 (347)
Q Consensus 6 ~~rywCh~C~~~V~-p~~~~e~~CP~C~sG 34 (347)
...|-|-.|.+.|. ......+.||+|++-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 45799999999996 333447999999984
No 107
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.81 E-value=0.28 Score=53.33 Aligned_cols=37 Identities=22% Similarity=0.661 Sum_probs=29.1
Q ss_pred ccccccchhhhhhhccCCceEEecCCCcccccchHHHH
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWL 247 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl 247 (347)
++....|.+|...+.. ..-.+-||+|.||+.||.+-.
T Consensus 814 ~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred ecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence 4456799999998854 455677899999999996543
No 108
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.75 E-value=0.31 Score=44.87 Aligned_cols=39 Identities=33% Similarity=0.701 Sum_probs=29.8
Q ss_pred chhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCcccC
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
|-+|.+.= ..+..+||.|+ +|..|-.. ...||+|+....
T Consensus 161 Cr~C~~~~---~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGERE---ATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcCC---ceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 88887765 77999999987 78888533 456999987653
No 109
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.15 E-value=0.62 Score=32.22 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=24.1
Q ss_pred cEeeecCCceeeecCCCCccCCCCCCCce
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
.|-|-.|..+|.....+.+.||.|++--+
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEE
Confidence 48999999999877666799999997533
No 110
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.14 E-value=0.57 Score=40.19 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=25.5
Q ss_pred CCcEeeecCCceeeecC--------------------CCCccCCCCCCCceEecC
Q 036250 6 VGSYWCYICSRMVNPRM--------------------EAGIKCPFCETGFVEQMS 40 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~--------------------~~e~~CP~C~sGFiEE~~ 40 (347)
..+|||..|.....+.- ...+.||.|++.-++-+.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 57899999998876541 224779999987766444
No 111
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=85.93 E-value=0.47 Score=34.33 Aligned_cols=38 Identities=26% Similarity=0.670 Sum_probs=31.0
Q ss_pred ccchhhhhhhccCCceEEec-CCCcccccchHHHHhcCCCCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMP-CKHKFHGECIMPWLELQSSCPI 255 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~ 255 (347)
..|.+|-+.|..++++++-| |+-.+|+.|..+ ...|-+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~ 44 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN 44 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence 47999999998888888888 999999999643 455544
No 112
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=85.64 E-value=0.53 Score=45.73 Aligned_cols=45 Identities=24% Similarity=0.609 Sum_probs=34.6
Q ss_pred ccccccchhhhhhhccCCceEEecC--CCcccccchHHHHhcCCCCCCCCcccC
Q 036250 210 IDQDLQCAVCLEEFVMGNEAKEMPC--KHKFHGECIMPWLELQSSCPICRYQLP 261 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~~~~~~lpC--~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (347)
+.+-++|+||.+.+. +-.+.| ||+-|..|-. +..+.||.||.++.
T Consensus 45 ~~~lleCPvC~~~l~----~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS----PPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred chhhccCchhhccCc----ccceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 344579999999983 335556 6999999975 36778999999886
No 113
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=85.26 E-value=0.26 Score=34.65 Aligned_cols=33 Identities=30% Similarity=0.703 Sum_probs=23.1
Q ss_pred EecCC-CcccccchHHHHhcCCCCCCCCcccCCC
Q 036250 231 EMPCK-HKFHGECIMPWLELQSSCPICRYQLPSD 263 (347)
Q Consensus 231 ~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (347)
.+.|. |..|..|+...|.....||+|.++|+..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 44575 9999999999999999999999999764
No 114
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.68 E-value=0.38 Score=50.66 Aligned_cols=44 Identities=32% Similarity=0.739 Sum_probs=33.0
Q ss_pred cccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcc
Q 036250 213 DLQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQ 259 (347)
Q Consensus 213 ~~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~ 259 (347)
-+.|.||+..|... -.++-|-|+|..|..|+..- .+.+|| |++.
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~D 55 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRD 55 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCcc
Confidence 35799998888532 36777889999999998664 456788 6553
No 115
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.41 E-value=0.88 Score=38.44 Aligned_cols=35 Identities=17% Similarity=0.290 Sum_probs=24.5
Q ss_pred CCcEeeecCCceeeecCCC------CccCCCCCCCceEecCC
Q 036250 6 VGSYWCYICSRMVNPRMEA------GIKCPFCETGFVEQMSS 41 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~------e~~CP~C~sGFiEE~~~ 41 (347)
..++|| .|.....+.... -+.||.|++..++-+..
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 578999 999886543110 15699999988775543
No 116
>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=82.29 E-value=1.1 Score=28.98 Aligned_cols=25 Identities=32% Similarity=0.693 Sum_probs=20.0
Q ss_pred EeeecCCceeeecCCCCccCCCCCC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
|-|-.|..+|.....+.+.||.|+.
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCC
Confidence 7799999999877666799999985
No 117
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.88 E-value=1.4 Score=30.39 Aligned_cols=32 Identities=28% Similarity=0.717 Sum_probs=24.4
Q ss_pred CcEeeecCCceeeecCCC-CccCCCCCCCceEe
Q 036250 7 GSYWCYICSRMVNPRMEA-GIKCPFCETGFVEQ 38 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~~~-e~~CP~C~sGFiEE 38 (347)
..|-|-.|-..+...... .+.||+|++-++-.
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFK 34 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEc
Confidence 368899999998654332 58999999888743
No 118
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=81.82 E-value=0.47 Score=50.78 Aligned_cols=30 Identities=30% Similarity=0.680 Sum_probs=25.1
Q ss_pred CCceEEecCCCcccccchHHHHhcCCCCCC
Q 036250 226 GNEAKEMPCKHKFHGECIMPWLELQSSCPI 255 (347)
Q Consensus 226 ~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~ 255 (347)
|...+...|+|+.|.+|...|++....||.
T Consensus 1040 gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1040 GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 344555679999999999999999999985
No 119
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.56 E-value=1.1 Score=47.03 Aligned_cols=47 Identities=36% Similarity=0.923 Sum_probs=39.5
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (347)
...|.||+... ..+..+|. |..|+.+|+..+..||+|+..+..++..
T Consensus 479 ~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~ 525 (543)
T KOG0802|consen 479 NDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFL 525 (543)
T ss_pred cCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccccc
Confidence 46899999998 45677788 8999999999999999999988666433
No 120
>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=79.25 E-value=1.1 Score=43.14 Aligned_cols=53 Identities=23% Similarity=0.584 Sum_probs=38.0
Q ss_pred cchhhhhhhccCCceE--EecCCCcccccchHHHHhcC-CCCCCCCcccCCCCCcc
Q 036250 215 QCAVCLEEFVMGNEAK--EMPCKHKFHGECIMPWLELQ-SSCPICRYQLPSDDLKV 267 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~--~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~~~~ 267 (347)
.|++|....-....++ .-+|+|..|.+|+..-+... ..||.|-..|-......
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 4888887654333333 33799999999999988655 56999988776655443
No 121
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=77.46 E-value=1.4 Score=42.80 Aligned_cols=27 Identities=26% Similarity=0.508 Sum_probs=20.3
Q ss_pred CCCCcEeeecCCceeeecCCCCccCCCCCCCc
Q 036250 4 ATVGSYWCYICSRMVNPRMEAGIKCPFCETGF 35 (347)
Q Consensus 4 ~~~~rywCh~C~~~V~p~~~~e~~CP~C~sGF 35 (347)
.+..+-+||.|...-+ +|+||+|+-=+
T Consensus 3 pts~~~~C~ic~vq~~-----~YtCPRCn~~Y 29 (383)
T KOG4317|consen 3 PTSSFLACGICGVQKR-----EYTCPRCNLLY 29 (383)
T ss_pred CCCceeeccccccccc-----cccCCCCCccc
Confidence 3456789999986654 69999998533
No 122
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=75.16 E-value=2.7 Score=27.75 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=19.6
Q ss_pred cEeeecCCceeeecC----CCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPRM----EAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~~----~~e~~CP~C~s 33 (347)
.|-|..|...+.... +..+.||.|++
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 688999999765332 33578999998
No 123
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=74.68 E-value=1.3 Score=43.51 Aligned_cols=55 Identities=20% Similarity=0.553 Sum_probs=36.7
Q ss_pred ccccchhhhhhhccCCc-eEEecCCCcccccchHHHH-hcCCCCCCCCcccCCCCCc
Q 036250 212 QDLQCAVCLEEFVMGNE-AKEMPCKHKFHGECIMPWL-ELQSSCPICRYQLPSDDLK 266 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~ 266 (347)
++.-|+.|++.+...++ ..--|||...|.-|...-- .....||-||+....+...
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~ 69 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVR 69 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccccee
Confidence 34569999999965433 3445688777776654433 2456799999977665544
No 124
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=74.38 E-value=1.4 Score=44.36 Aligned_cols=22 Identities=32% Similarity=0.751 Sum_probs=19.0
Q ss_pred ecCCceeeecCCCCccCCCCCCCceE
Q 036250 12 YICSRMVNPRMEAGIKCPFCETGFVE 37 (347)
Q Consensus 12 h~C~~~V~p~~~~e~~CP~C~sGFiE 37 (347)
|+|.|.|. .||+||.|+.-|-.
T Consensus 286 HrC~RIV~----vEYrCPEC~KVFsC 307 (500)
T KOG3993|consen 286 HRCPRIVH----VEYRCPECDKVFSC 307 (500)
T ss_pred ccCCeeEE----eeecCCcccccccC
Confidence 88999987 37999999999965
No 125
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=74.28 E-value=0.58 Score=49.88 Aligned_cols=47 Identities=28% Similarity=0.730 Sum_probs=37.0
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCC---CCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQS---SCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~ 262 (347)
.++|+||+..+ ..+..+.|.|.|+..|+..-+...+ .||+|+..+..
T Consensus 21 ~lEc~ic~~~~---~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 21 ILECPICLEHV---KEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK 70 (684)
T ss_pred hccCCceeEEe---eccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence 46899999999 5557888999999999976665443 59999966543
No 126
>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=73.17 E-value=1.2 Score=32.47 Aligned_cols=32 Identities=25% Similarity=0.559 Sum_probs=21.3
Q ss_pred CCCCcEeeecCCceeeecCCCCccCCCCCCCceE
Q 036250 4 ATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVE 37 (347)
Q Consensus 4 ~~~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiE 37 (347)
|.--+|-|--|..=+.-.+ ..+||.|+|+||.
T Consensus 22 A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~ 53 (57)
T PF06906_consen 22 AYICSFECTFCADCAETML--NGVCPNCGGELVR 53 (57)
T ss_pred ceEEeEeCcccHHHHHHHh--cCcCcCCCCcccc
Confidence 3344566666665555444 3789999999984
No 127
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=72.73 E-value=1.2 Score=42.86 Aligned_cols=32 Identities=22% Similarity=0.595 Sum_probs=24.4
Q ss_pred CCCcccccchHHHHhc-------------CCCCCCCCcccCCCCC
Q 036250 234 CKHKFHGECIMPWLEL-------------QSSCPICRYQLPSDDL 265 (347)
Q Consensus 234 C~H~Fh~~Ci~~Wl~~-------------~~~CP~CR~~l~~~~~ 265 (347)
|..++|.+|+-+|+.. +-+||.||+.+...+.
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 6678899999888743 3459999998876544
No 128
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=72.25 E-value=2.2 Score=38.54 Aligned_cols=28 Identities=29% Similarity=0.740 Sum_probs=20.8
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEe
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
..-|||-.|+-.+. .-.|+-|+++|-|-
T Consensus 12 ~~iyWCe~cNlPl~-----~~~c~~cg~~~~~l 39 (202)
T COG5270 12 FPIYWCEKCNLPLL-----GRRCSVCGSKVEEL 39 (202)
T ss_pred cceeehhhCCCccc-----cccccccCCcceEE
Confidence 34699999998763 35699999776443
No 129
>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=71.43 E-value=3 Score=29.50 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=19.6
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhc---CC--CCCCCCcc
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL---QS--SCPICRYQ 259 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~---~~--~CP~CR~~ 259 (347)
+.|+|....+. .-++...|.|+-|.+ +..||+. .. .||+|.++
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 46888888883 234445599985543 4566643 22 49999763
No 130
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=70.76 E-value=1.7 Score=47.02 Aligned_cols=49 Identities=14% Similarity=0.188 Sum_probs=34.2
Q ss_pred ccchhhhhhhccCC-ceEEec---CCCcccccchHHHHhc------CCCCCCCCcccCC
Q 036250 214 LQCAVCLEEFVMGN-EAKEMP---CKHKFHGECIMPWLEL------QSSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~~-~~~~lp---C~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~ 262 (347)
..|.||.-++.... ..-.+| |.|.||..||..|+.. +-.|+.|...|..
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s 155 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS 155 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence 46777777774311 133445 9999999999999854 3358999887643
No 131
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=70.13 E-value=1.6 Score=47.24 Aligned_cols=51 Identities=33% Similarity=0.825 Sum_probs=38.1
Q ss_pred cccchhhhhhhccCCceEEecCC-----CcccccchHHHHhcC--CCCCCCCcccCCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCK-----HKFHGECIMPWLELQ--SSCPICRYQLPSDD 264 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~~~ 264 (347)
+..|-||..+=.. +.+---||+ ...|.+|+..|++-. ..|-+|+.++.-++
T Consensus 12 ~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 12 KRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD 69 (1175)
T ss_pred chhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence 4689999988654 345556776 358999999999754 46999999875554
No 132
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=68.95 E-value=2.6 Score=45.36 Aligned_cols=44 Identities=25% Similarity=0.479 Sum_probs=31.5
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCC--CCc
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPI--CRY 258 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~--CR~ 258 (347)
..|.+|-..+. |..+-.--|+|.-|..|+.+|+..+..||. |-+
T Consensus 780 ~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~ 825 (839)
T KOG0269|consen 780 AKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPH 825 (839)
T ss_pred cCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCccccCCc
Confidence 36778876662 222222239999999999999999988877 643
No 133
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=68.60 E-value=1.4 Score=42.14 Aligned_cols=50 Identities=26% Similarity=0.595 Sum_probs=36.7
Q ss_pred ccchhhhhhhccCCc-eEEecCC-----CcccccchHHHHhc--CCCCCCCCcccCCC
Q 036250 214 LQCAVCLEEFVMGNE-AKEMPCK-----HKFHGECIMPWLEL--QSSCPICRYQLPSD 263 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~-~~~lpC~-----H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~~ 263 (347)
..|=||.++...... ..+.||. +..|..|+..|+.. ...|-+|.......
T Consensus 79 ~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 79 PICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 579999997743221 5677864 66899999999974 45699998866444
No 134
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=68.56 E-value=2.3 Score=25.26 Aligned_cols=22 Identities=27% Similarity=0.677 Sum_probs=17.2
Q ss_pred eeecCCceeeecCCCCccCCCCCCC
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
+|..|-.+|.. ....||.|+.-
T Consensus 1 ~Cp~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC---cCcchhhhCCc
Confidence 68999999962 35789999864
No 135
>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=68.18 E-value=2.8 Score=25.67 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=17.9
Q ss_pred eecCCceeeecCCCCccCCCCCCCce
Q 036250 11 CYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
|-.|..+|... ..+||+|+--|.
T Consensus 3 CP~C~~~V~~~---~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPES---AKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchhh---cCcCCCCCCCCc
Confidence 77899999522 478999998774
No 136
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.77 E-value=1.8 Score=43.57 Aligned_cols=38 Identities=21% Similarity=0.647 Sum_probs=27.1
Q ss_pred cccchhhh-hhhccCCceEEecCCCcccccchHHHHhcC
Q 036250 213 DLQCAVCL-EEFVMGNEAKEMPCKHKFHGECIMPWLELQ 250 (347)
Q Consensus 213 ~~~C~ICl-~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (347)
..+|.||. +...........-|+|.||.+|+.+.++.+
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 46899999 444332333445699999999999888643
No 137
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=65.01 E-value=3.7 Score=26.61 Aligned_cols=27 Identities=22% Similarity=0.407 Sum_probs=20.5
Q ss_pred EeeecCCceeee-cCCCCccCCCCCCCc
Q 036250 9 YWCYICSRMVNP-RMEAGIKCPFCETGF 35 (347)
Q Consensus 9 ywCh~C~~~V~p-~~~~e~~CP~C~sGF 35 (347)
.-|..|...... .-.+.++|+.|+.-|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 458889998765 445579999998755
No 138
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=62.53 E-value=5 Score=37.02 Aligned_cols=43 Identities=26% Similarity=0.682 Sum_probs=34.2
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
..|.+|...+-.| .+-=.|+-.+|..|+...+.....||.|..
T Consensus 182 k~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 182 KNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 4799999998422 233458888999999999999999999943
No 139
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.66 E-value=5.3 Score=38.98 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=35.3
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhc---CCCCCCCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL---QSSCPICR 257 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR 257 (347)
-..|+|-.+.-.....++.|.|+|+.-..-+....+. ...||+|-
T Consensus 336 ~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 336 LFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 4689998888877778999999999988887765433 33599994
No 140
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=60.64 E-value=6.6 Score=35.26 Aligned_cols=32 Identities=28% Similarity=0.551 Sum_probs=24.5
Q ss_pred CCcEeeecCCceeeec--CCCCccCCCCCCCceE
Q 036250 6 VGSYWCYICSRMVNPR--MEAGIKCPFCETGFVE 37 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~--~~~e~~CP~C~sGFiE 37 (347)
..-|.|-.|...++-. +..+.+||.|++-.+|
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 4578899999888532 3457999999987766
No 141
>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=59.41 E-value=3.5 Score=38.77 Aligned_cols=49 Identities=27% Similarity=0.632 Sum_probs=37.0
Q ss_pred cccchhhhhhhccCCceEEe--c-CCCcccccchHHHHhcCC-CCC--CCCcccC
Q 036250 213 DLQCAVCLEEFVMGNEAKEM--P-CKHKFHGECIMPWLELQS-SCP--ICRYQLP 261 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~l--p-C~H~Fh~~Ci~~Wl~~~~-~CP--~CR~~l~ 261 (347)
+..|+||..+--...+++.| | |-|.+|.+|++.-+.... .|| -|-+-|-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 34799999876555555544 6 999999999999997654 699 7866553
No 142
>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=59.22 E-value=5.4 Score=32.72 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=22.8
Q ss_pred CCCcCCCCCCCCcCCCCCCCCCCCCCCCCCCcCCCccccCC
Q 036250 299 RRNWIPIPWPFDGLLSMSGSQEGGTSNSESSAAGTAVAGAG 339 (347)
Q Consensus 299 rr~~~s~~~pf~~~f~~s~~~~~~~s~~~~ss~~~~~~~~g 339 (347)
.--|.-+-|||+.+|++.+. ..+|.+|+++..-|
T Consensus 49 kwiwhgitwpfrklfgsrse-------apssttnatgntng 82 (141)
T PF07860_consen 49 KWIWHGITWPFRKLFGSRSE-------APSSTTNATGNTNG 82 (141)
T ss_pred hhhhhcccchHHHHhCCccc-------CCcccccCccCcCC
Confidence 34578899999999986644 45556666633333
No 143
>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=57.30 E-value=10 Score=25.66 Aligned_cols=27 Identities=22% Similarity=0.644 Sum_probs=18.4
Q ss_pred cEeeecCCceeeec--C--CCCccCCCCCCC
Q 036250 8 SYWCYICSRMVNPR--M--EAGIKCPFCETG 34 (347)
Q Consensus 8 rywCh~C~~~V~p~--~--~~e~~CP~C~sG 34 (347)
.|-|-.|....... + +..+.||.|++.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 58899998554322 2 235889999984
No 144
>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=56.63 E-value=6.9 Score=30.10 Aligned_cols=30 Identities=23% Similarity=0.587 Sum_probs=14.3
Q ss_pred EeeecCCceeeecCCCCccCCCCCCCceEecC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCETGFVEQMS 40 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~ 40 (347)
++||.|-.... .+. -..||.|+..=+.-+.
T Consensus 10 lrC~aCf~~t~-~~~-k~FCp~CGn~TL~rvs 39 (73)
T PF08772_consen 10 LRCHACFKITK-DMT-KQFCPKCGNATLKRVS 39 (73)
T ss_dssp EE-SSS--EES--SS---S-SSS--S--EEEE
T ss_pred EEccccccCcC-CCC-ceeCcccCCCcceEEE
Confidence 57999999886 333 5889999988776664
No 145
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.58 E-value=6.7 Score=27.26 Aligned_cols=29 Identities=24% Similarity=0.666 Sum_probs=21.1
Q ss_pred eeecCCceeeecCC---CCccCCCCCCCceEecC
Q 036250 10 WCYICSRMVNPRME---AGIKCPFCETGFVEQMS 40 (347)
Q Consensus 10 wCh~C~~~V~p~~~---~e~~CP~C~sGFiEE~~ 40 (347)
||-.|...+.+... ..++||.|+ |++.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 89999998866532 148899998 555554
No 146
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.73 E-value=5.4 Score=40.11 Aligned_cols=43 Identities=23% Similarity=0.477 Sum_probs=31.4
Q ss_pred ccchhhhhhhccCCc--eEEecCCCcccccchHHHHhcCCCCCCC
Q 036250 214 LQCAVCLEEFVMGNE--AKEMPCKHKFHGECIMPWLELQSSCPIC 256 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (347)
..|++|.-.++.... ...-.|+|.||+.|...|......|..|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 579998887754332 3333499999999999998777767555
No 147
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.43 E-value=9.6 Score=36.73 Aligned_cols=38 Identities=26% Similarity=0.411 Sum_probs=27.9
Q ss_pred cccchhhhhhhccCCceEEec--CCCcccccchHHHHhcCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMP--CKHKFHGECIMPWLELQS 251 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~~~~ 251 (347)
.+.|.+|.|.+++ ...++-| =.|.||..|-..-++.+.
T Consensus 268 pLcCTLC~ERLED-THFVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 268 PLCCTLCHERLED-THFVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred ceeehhhhhhhcc-CceeecCCCcccceecccCHHHHHhhc
Confidence 4789999999943 3333333 379999999999887643
No 148
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=54.35 E-value=5 Score=43.50 Aligned_cols=46 Identities=24% Similarity=0.541 Sum_probs=32.6
Q ss_pred ccccccchhhhhhhccC----CceEEecCCCcccccchHHHHhcCCCCCCC
Q 036250 210 IDQDLQCAVCLEEFVMG----NEAKEMPCKHKFHGECIMPWLELQSSCPIC 256 (347)
Q Consensus 210 ~~~~~~C~ICl~~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (347)
+.-+..|.-|.+..... ..++.+-|+|.||..|+.--..++. |-.|
T Consensus 781 v~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 781 VSVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred EeehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 33345799999887522 4578888999999999966654444 5555
No 149
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=53.27 E-value=5.4 Score=26.05 Aligned_cols=23 Identities=26% Similarity=0.804 Sum_probs=12.3
Q ss_pred eeecCCceeeecCC--CC---ccCCCCC
Q 036250 10 WCYICSRMVNPRME--AG---IKCPFCE 32 (347)
Q Consensus 10 wCh~C~~~V~p~~~--~e---~~CP~C~ 32 (347)
||-+|-..+...++ ++ .+||.|+
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 78889888866654 22 8899885
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=52.03 E-value=9.3 Score=33.56 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=24.3
Q ss_pred CCcEeeecCCceeeec--CCCCccCCCCCCCceEecC
Q 036250 6 VGSYWCYICSRMVNPR--MEAGIKCPFCETGFVEQMS 40 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~--~~~e~~CP~C~sGFiEE~~ 40 (347)
..-|.|-.|...++-. +..+.+||.|++- +++++
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~-L~~~d 142 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAM-LDYLD 142 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCE-eeecc
Confidence 4568899999887522 3447999999986 44444
No 151
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.83 E-value=7 Score=23.66 Aligned_cols=23 Identities=22% Similarity=0.639 Sum_probs=16.2
Q ss_pred EeeecCCceeeecCCCCccCCCCCCC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
.+|..|...|. .++-.||.|+.-
T Consensus 3 ~~Cp~Cg~~~~---~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID---PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC---cccccChhhCCC
Confidence 36888988654 236779999753
No 152
>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=50.84 E-value=8.6 Score=27.30 Aligned_cols=11 Identities=45% Similarity=1.515 Sum_probs=8.1
Q ss_pred CccCCCCCCCc
Q 036250 25 GIKCPFCETGF 35 (347)
Q Consensus 25 e~~CP~C~sGF 35 (347)
.+.||+|+.+|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 47788888755
No 153
>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=50.23 E-value=7.2 Score=25.79 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=8.4
Q ss_pred CccCCCCCCC
Q 036250 25 GIKCPFCETG 34 (347)
Q Consensus 25 e~~CP~C~sG 34 (347)
++.||+|++-
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 6889999983
No 154
>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=49.71 E-value=14 Score=26.30 Aligned_cols=26 Identities=31% Similarity=0.860 Sum_probs=17.5
Q ss_pred cEeeecCCceeeec----------------CCCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPR----------------MEAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~----------------~~~e~~CP~C~s 33 (347)
+|-|-.|-=...+. ++++.+||.|+.
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 35566776666653 466788998875
No 155
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.48 E-value=4.1 Score=38.65 Aligned_cols=50 Identities=24% Similarity=0.596 Sum_probs=34.5
Q ss_pred cccchhhhhhhccCCce-EEecCC-----CcccccchHHHHhcCC--------CCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEA-KEMPCK-----HKFHGECIMPWLELQS--------SCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~-~~lpC~-----H~Fh~~Ci~~Wl~~~~--------~CP~CR~~l~~ 262 (347)
+..|-||+..=++.... -+-||. |..|..||..|+..+. +||-|+.+...
T Consensus 20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii 83 (293)
T KOG3053|consen 20 ERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII 83 (293)
T ss_pred ceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence 45799999876433222 234663 7899999999995432 49999887543
No 156
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=49.31 E-value=9 Score=28.72 Aligned_cols=18 Identities=28% Similarity=0.737 Sum_probs=14.9
Q ss_pred eecCCceeeecCCCCccCCCCCC
Q 036250 11 CYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~s 33 (347)
|..|++-+. +-+||.|++
T Consensus 8 C~~C~~i~~-----~~~Cp~Cgs 25 (64)
T PRK06393 8 CKKCKRLTP-----EKTCPVHGD 25 (64)
T ss_pred HhhCCcccC-----CCcCCCCCC
Confidence 889998883 348999999
No 157
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.43 E-value=7.9 Score=36.60 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=29.0
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHh
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE 248 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~ 248 (347)
..|+.||..+ .++++.|=||+|+..||+.++.
T Consensus 44 dcCsLtLqPc---~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 44 DCCSLTLQPC---RDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ceeeeecccc---cCCccCCCCeeeeHHHHHHHHH
Confidence 5799999999 8899999999999999988863
No 158
>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=47.72 E-value=20 Score=24.92 Aligned_cols=32 Identities=19% Similarity=0.466 Sum_probs=21.9
Q ss_pred cEeeecCCceeeecC--C--CCccCCCCCCCceEec
Q 036250 8 SYWCYICSRMVNPRM--E--AGIKCPFCETGFVEQM 39 (347)
Q Consensus 8 rywCh~C~~~V~p~~--~--~e~~CP~C~sGFiEE~ 39 (347)
.|.|-.|......+. . ..+.||.|++.=++.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 588999999665443 1 2467999999544444
No 159
>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=47.60 E-value=7.3 Score=24.39 Aligned_cols=22 Identities=27% Similarity=0.866 Sum_probs=17.6
Q ss_pred EeeecCCceeeecCCCCccCCCCC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCE 32 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~ 32 (347)
|||-.|.+.+.... -|.|-.|.
T Consensus 1 ~~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE--eEEeCCCC
Confidence 78999999997553 58888887
No 160
>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=47.11 E-value=17 Score=25.50 Aligned_cols=27 Identities=26% Similarity=0.802 Sum_probs=15.8
Q ss_pred cEeeecCCceeeec----------------CCCCccCCCCCCC
Q 036250 8 SYWCYICSRMVNPR----------------MEAGIKCPFCETG 34 (347)
Q Consensus 8 rywCh~C~~~V~p~----------------~~~e~~CP~C~sG 34 (347)
+|-|-.|-=...+. |+++.+||.|+.+
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 46777777555544 3557899999753
No 161
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=46.91 E-value=14 Score=27.22 Aligned_cols=22 Identities=32% Similarity=0.762 Sum_probs=9.1
Q ss_pred eeecCCceeeecC-CCCccCCCC
Q 036250 10 WCYICSRMVNPRM-EAGIKCPFC 31 (347)
Q Consensus 10 wCh~C~~~V~p~~-~~e~~CP~C 31 (347)
.|-.|.+.|.+.- .....||.|
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnC 31 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNC 31 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCC
Confidence 4444444444332 223444444
No 162
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.61 E-value=14 Score=36.34 Aligned_cols=46 Identities=24% Similarity=0.451 Sum_probs=31.7
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
...|-.|.++...+...+--.|+|.||.+|=.--=+.-..||-|..
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 3469999777765444444559999999995433244456999964
No 163
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=46.33 E-value=11 Score=27.91 Aligned_cols=19 Identities=26% Similarity=0.805 Sum_probs=15.0
Q ss_pred eeecCCceeeecCCCCccCCCCCC
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
=|..|++-+. +-.||.|++
T Consensus 5 AC~~C~~i~~-----~~~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYITT-----EDRCPVCGS 23 (61)
T ss_pred hhhhCCcccC-----CCcCCCCcC
Confidence 4889998873 337999998
No 164
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=45.95 E-value=6.7 Score=28.03 Aligned_cols=28 Identities=32% Similarity=0.693 Sum_probs=19.6
Q ss_pred CcEeeecCCceeeec---CCCCccCCCCCCC
Q 036250 7 GSYWCYICSRMVNPR---MEAGIKCPFCETG 34 (347)
Q Consensus 7 ~rywCh~C~~~V~p~---~~~e~~CP~C~sG 34 (347)
..+-|-.|.+-.--. ..-+|+||+|..=
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 456788999877432 1237999999873
No 165
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=45.93 E-value=18 Score=31.25 Aligned_cols=33 Identities=21% Similarity=0.467 Sum_probs=23.2
Q ss_pred CCcEeeecCCceeeec----C---CCCccCCCCCCCceEe
Q 036250 6 VGSYWCYICSRMVNPR----M---EAGIKCPFCETGFVEQ 38 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~----~---~~e~~CP~C~sGFiEE 38 (347)
...|.|-.|...+... + ...++||.|+.-.++.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 4578999999888632 1 1138999999866553
No 166
>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=45.43 E-value=16 Score=23.01 Aligned_cols=36 Identities=28% Similarity=0.527 Sum_probs=23.4
Q ss_pred chhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCccc
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
|..|...+.... .....=+..||..|. .|..|...|
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 777888775432 223334678998875 688887766
No 167
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=44.53 E-value=13 Score=33.91 Aligned_cols=41 Identities=29% Similarity=0.789 Sum_probs=26.4
Q ss_pred cccchhhhhh-----hccCCceEEecCCCcccccchHHHHhcCCCCCCCCc
Q 036250 213 DLQCAVCLEE-----FVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 213 ~~~C~ICl~~-----~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
...|-||.+. |+.....+--.|+-+||..|.. ...||.|..
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 4577788752 3332223333499999999975 367999943
No 168
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=44.33 E-value=14 Score=36.36 Aligned_cols=49 Identities=20% Similarity=0.488 Sum_probs=35.9
Q ss_pred ccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 214 LQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 214 ~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
..|+||-+..... ....-.||++..|..|+..-...+..||.||++...
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYER 299 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcccc
Confidence 5899999988432 223333488888888888888888999999965543
No 169
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.25 E-value=7.1 Score=39.91 Aligned_cols=36 Identities=31% Similarity=0.677 Sum_probs=29.8
Q ss_pred ccccchhhhhhhccCCceEEecCCCcccccchHHHHhc
Q 036250 212 QDLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLEL 249 (347)
Q Consensus 212 ~~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~ 249 (347)
...+|-||.+.+.. ....+.|+|.||..|+...|..
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 34689999999843 5778889999999999988864
No 170
>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=43.63 E-value=13 Score=37.73 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=18.4
Q ss_pred eeecCCceeeecCCCCccCCCCCCCc
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCETGF 35 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~sGF 35 (347)
=||.|...+.+ +....||||+.--
T Consensus 217 ~C~~Cd~~~~~--~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTILP--AQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCccCC--CCCcCCcCCCCcc
Confidence 49999997753 4467899999754
No 171
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.58 E-value=7.6 Score=29.79 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=21.1
Q ss_pred CCCCcEeeecCCceeeecCCCCccCCCCCCCceEe
Q 036250 4 ATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 4 ~~~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
|+..+|-|--|..-+.-++. -.||.|+++||--
T Consensus 22 A~ICtfEcTFCadCae~~l~--g~CPnCGGelv~R 54 (84)
T COG3813 22 ARICTFECTFCADCAENRLH--GLCPNCGGELVAR 54 (84)
T ss_pred eeEEEEeeehhHhHHHHhhc--CcCCCCCchhhcC
Confidence 44456666666555544443 5799999998753
No 172
>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=42.46 E-value=15 Score=24.87 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=9.9
Q ss_pred ccCCCCCCCceEe
Q 036250 26 IKCPFCETGFVEQ 38 (347)
Q Consensus 26 ~~CP~C~sGFiEE 38 (347)
++||.|++..|++
T Consensus 1 m~Cp~Cg~~~~~~ 13 (43)
T PF08271_consen 1 MKCPNCGSKEIVF 13 (43)
T ss_dssp ESBTTTSSSEEEE
T ss_pred CCCcCCcCCceEE
Confidence 5799999987533
No 173
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=42.38 E-value=17 Score=34.74 Aligned_cols=50 Identities=24% Similarity=0.531 Sum_probs=32.6
Q ss_pred ccchhhhhhhccCCceE-Eec---CCCcccccchHHHHhc---------CCCCCCCCcccCCC
Q 036250 214 LQCAVCLEEFVMGNEAK-EMP---CKHKFHGECIMPWLEL---------QSSCPICRYQLPSD 263 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~-~lp---C~H~Fh~~Ci~~Wl~~---------~~~CP~CR~~l~~~ 263 (347)
..|.+|.+++...+..+ .-+ |.-++|..|+-.-+.. ...||.|++.+.-.
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~w~ 245 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLSWT 245 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceeeHH
Confidence 58999999994322222 111 7788999999774422 23499999865433
No 174
>PRK12495 hypothetical protein; Provisional
Probab=41.94 E-value=14 Score=34.32 Aligned_cols=32 Identities=25% Similarity=0.487 Sum_probs=25.6
Q ss_pred CCCCcEeeecCCceeeecCCCCccCCCCCCCce
Q 036250 4 ATVGSYWCYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 4 ~~~~rywCh~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
+....|+|-.|-..|- .++..++||.|+.-+-
T Consensus 38 atmsa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 38 ATMTNAHCDECGDPIF-RHDGQEFCPTCQQPVT 69 (226)
T ss_pred cccchhhcccccCccc-CCCCeeECCCCCCccc
Confidence 3467899999999995 6676899999996544
No 175
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=41.50 E-value=15 Score=24.58 Aligned_cols=25 Identities=28% Similarity=0.704 Sum_probs=19.5
Q ss_pred eecCCceeeecCCCCccCCCCCCCceEe
Q 036250 11 CYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
|+.|.+.+... + ++|.+|+.-|-.+
T Consensus 1 C~~C~~~~~l~-~--f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT-G--FKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc-C--eECCccCCccccc
Confidence 78899887632 4 8899999988654
No 176
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=41.45 E-value=13 Score=35.94 Aligned_cols=37 Identities=30% Similarity=0.673 Sum_probs=28.3
Q ss_pred ccchhhhhhhccCCceEEecCCCcccccchHHHHhcC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQ 250 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (347)
..|.+|+++|..+.......|.-+||..|+..|+...
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred eecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 3899999999765566666676689999998887544
No 177
>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=41.29 E-value=16 Score=25.52 Aligned_cols=40 Identities=28% Similarity=0.499 Sum_probs=27.5
Q ss_pred chhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCC
Q 036250 216 CAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDD 264 (347)
Q Consensus 216 C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (347)
|..|...+.. ...+...-+..||..|. .|-.|+..|....
T Consensus 1 C~~C~~~I~~-~~~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYG-TEIVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESS-SSEEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccC-cEEEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 6677777753 23333357788998886 7889988886654
No 178
>PF14968 CCDC84: Coiled coil protein 84
Probab=39.83 E-value=14 Score=36.47 Aligned_cols=34 Identities=24% Similarity=0.662 Sum_probs=25.0
Q ss_pred CCCCcEeeecCCceeeecCCCCccCCCCCCCceEecCCC
Q 036250 4 ATVGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSSS 42 (347)
Q Consensus 4 ~~~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~~ 42 (347)
+...+||||.|..+|.-... -+.| +|.||-|...
T Consensus 54 ~~~~~fWC~fC~~ev~~~~s-~~~~----~~ai~HLaS~ 87 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREHDS-SFAC----GGAIEHLASP 87 (336)
T ss_pred cccceeEeeCccchhhhccc-hhhh----ccHHhhcCCH
Confidence 34679999999999974433 3444 7889998764
No 179
>PHA00616 hypothetical protein
Probab=39.38 E-value=8 Score=26.83 Aligned_cols=12 Identities=25% Similarity=0.503 Sum_probs=10.2
Q ss_pred ccCCCCCCCceE
Q 036250 26 IKCPFCETGFVE 37 (347)
Q Consensus 26 ~~CP~C~sGFiE 37 (347)
+.||+|+..|+.
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 679999999975
No 180
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.02 E-value=13 Score=27.57 Aligned_cols=13 Identities=31% Similarity=1.066 Sum_probs=10.6
Q ss_pred CCccCCCCCCCce
Q 036250 24 AGIKCPFCETGFV 36 (347)
Q Consensus 24 ~e~~CP~C~sGFi 36 (347)
.|++||+|+.-|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 4799999997663
No 181
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=38.56 E-value=8.9 Score=40.57 Aligned_cols=42 Identities=26% Similarity=0.692 Sum_probs=26.5
Q ss_pred cccchhhhh-----hhccCCceEEecCCCcccccchHHHHhcCCCCCCCC
Q 036250 213 DLQCAVCLE-----EFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICR 257 (347)
Q Consensus 213 ~~~C~ICl~-----~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (347)
...|.||.. .|+.....+-..|+++||..|+.. ....||.|-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~ 557 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCE 557 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence 356777732 222233445556999999999644 344499993
No 182
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=38.08 E-value=18 Score=35.40 Aligned_cols=26 Identities=35% Similarity=0.846 Sum_probs=20.9
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
.+-|+|-.|+..|- .++ +.||.|+-.
T Consensus 306 ~gGy~CP~CktkVC-sLP--i~CP~Csl~ 331 (421)
T COG5151 306 GGGYECPVCKTKVC-SLP--ISCPICSLQ 331 (421)
T ss_pred cCceeCCcccceee-cCC--ccCcchhHH
Confidence 46799999999996 566 889999743
No 183
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=37.86 E-value=14 Score=24.28 Aligned_cols=11 Identities=55% Similarity=1.204 Sum_probs=8.2
Q ss_pred ccCCCCCCCce
Q 036250 26 IKCPFCETGFV 36 (347)
Q Consensus 26 ~~CP~C~sGFi 36 (347)
+.||.|+..|-
T Consensus 3 i~CP~C~~~f~ 13 (37)
T PF13719_consen 3 ITCPNCQTRFR 13 (37)
T ss_pred EECCCCCceEE
Confidence 57888887773
No 184
>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=37.24 E-value=34 Score=21.80 Aligned_cols=25 Identities=24% Similarity=0.703 Sum_probs=18.8
Q ss_pred cEeeecCCceeeecCCCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
+|-|-.|--...+... +.+||.|+.
T Consensus 1 ~~~C~~CGy~y~~~~~-~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEA-PWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcC-CCcCcCCCC
Confidence 3668888877776544 678999986
No 185
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.04 E-value=16 Score=34.55 Aligned_cols=26 Identities=31% Similarity=0.733 Sum_probs=21.0
Q ss_pred eecCCceeeecCC------CCccCCCCCCCce
Q 036250 11 CYICSRMVNPRME------AGIKCPFCETGFV 36 (347)
Q Consensus 11 Ch~C~~~V~p~~~------~e~~CP~C~sGFi 36 (347)
|+.|.+...|+.. +|+.||.|.-.|-
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 9999999887753 3899999998664
No 186
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=36.78 E-value=23 Score=25.16 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=24.3
Q ss_pred CCcEeee--cCCceeeec---CCCCccCCCCCCCceEec
Q 036250 6 VGSYWCY--ICSRMVNPR---MEAGIKCPFCETGFVEQM 39 (347)
Q Consensus 6 ~~rywCh--~C~~~V~p~---~~~e~~CP~C~sGFiEE~ 39 (347)
...-||. .|...|... ....++||.|+--|.-.-
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C 54 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRC 54 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCC
Confidence 3556999 999888654 233588999998886443
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=36.59 E-value=27 Score=23.80 Aligned_cols=23 Identities=22% Similarity=0.460 Sum_probs=14.8
Q ss_pred eeecCCceeeecCCCCccCCCCC
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCE 32 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~ 32 (347)
.|..|....-.....++.||.|+
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCCC
Confidence 48888655433233468899885
No 188
>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=36.03 E-value=28 Score=28.74 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=22.7
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEe
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
+.-.-|..|....-=+.-.-++||.|+.-|--+
T Consensus 7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 344569888766522322358899999999877
No 189
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=35.77 E-value=15 Score=27.72 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=8.6
Q ss_pred cccccchHHHHh
Q 036250 237 KFHGECIMPWLE 248 (347)
Q Consensus 237 ~Fh~~Ci~~Wl~ 248 (347)
-||..||.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 399999999984
No 190
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=35.55 E-value=16 Score=26.18 Aligned_cols=29 Identities=24% Similarity=0.710 Sum_probs=14.3
Q ss_pred eeecCCceeeecCC-----CCccCCCCCCCceEe
Q 036250 10 WCYICSRMVNPRME-----AGIKCPFCETGFVEQ 38 (347)
Q Consensus 10 wCh~C~~~V~p~~~-----~e~~CP~C~sGFiEE 38 (347)
+|+.|.+.+..... .-|.||.|..-|--+
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~d 34 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCID 34 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccC
Confidence 58888888754321 248899988877543
No 191
>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=34.51 E-value=27 Score=25.64 Aligned_cols=35 Identities=14% Similarity=0.407 Sum_probs=17.2
Q ss_pred cccchhhhhhhccCCceEEe-cCCCcccccchHHHH
Q 036250 213 DLQCAVCLEEFVMGNEAKEM-PCKHKFHGECIMPWL 247 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl 247 (347)
...|.+|...|..-..-..- -||++||..|....+
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 46899999999543222222 299999999986554
No 192
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=34.23 E-value=29 Score=34.16 Aligned_cols=29 Identities=34% Similarity=0.878 Sum_probs=21.5
Q ss_pred CCCcEeeecCCceeeecCCCCccCCCCCCCce
Q 036250 5 TVGSYWCYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 5 ~~~rywCh~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
...-|+|-+|...|- .+| +.||.|+--.|
T Consensus 273 ~~~Gy~CP~CkakvC-sLP--~eCpiC~ltLV 301 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVC-SLP--IECPICSLTLV 301 (378)
T ss_pred ccCceeCCcccCeee-cCC--ccCCccceeEe
Confidence 345699999999986 566 77999975443
No 193
>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 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=33.08 E-value=23 Score=28.76 Aligned_cols=26 Identities=31% Similarity=0.805 Sum_probs=18.0
Q ss_pred eecCCceeeecCCCCccCCCCCCCceE
Q 036250 11 CYICSRMVNPRMEAGIKCPFCETGFVE 37 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~sGFiE 37 (347)
|..|+..+...--.+-.||.|+ +|++
T Consensus 6 C~~C~~I~~~~qf~~~gCpnC~-~~l~ 31 (98)
T cd07973 6 CLLCSLIKTEDQFERDGCPNCE-GYLD 31 (98)
T ss_pred hccCCcccccccccCCCCCCCc-chhc
Confidence 8899988753322245799998 6664
No 195
>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=32.57 E-value=10 Score=21.58 Aligned_cols=11 Identities=45% Similarity=1.204 Sum_probs=7.3
Q ss_pred ccCCCCCCCce
Q 036250 26 IKCPFCETGFV 36 (347)
Q Consensus 26 ~~CP~C~sGFi 36 (347)
++||.|+..|-
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 46777776663
No 196
>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=32.34 E-value=38 Score=24.72 Aligned_cols=46 Identities=24% Similarity=0.505 Sum_probs=31.9
Q ss_pred cchhhhhhhccCC-ceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 215 QCAVCLEEFVMGN-EAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 215 ~C~ICl~~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
.|-.|-.++..+. ++++-.=...||.+|....| ++.||.|-..|..
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 4667777776554 44443323569999998876 7889999877643
No 197
>PF14353 CpXC: CpXC protein
Probab=32.24 E-value=26 Score=29.18 Aligned_cols=18 Identities=33% Similarity=0.681 Sum_probs=15.0
Q ss_pred CccCCCCCCCceEecCCC
Q 036250 25 GIKCPFCETGFVEQMSSS 42 (347)
Q Consensus 25 e~~CP~C~sGFiEE~~~~ 42 (347)
+++||.|+.-|--++..-
T Consensus 1 ~itCP~C~~~~~~~v~~~ 18 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTS 18 (128)
T ss_pred CcCCCCCCCeeEEEEEeE
Confidence 478999999999888643
No 198
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=32.09 E-value=41 Score=24.87 Aligned_cols=27 Identities=19% Similarity=0.556 Sum_probs=13.6
Q ss_pred CCcEeeecCCc-eeee-----cCCCCccCCCCC
Q 036250 6 VGSYWCYICSR-MVNP-----RMEAGIKCPFCE 32 (347)
Q Consensus 6 ~~rywCh~C~~-~V~p-----~~~~e~~CP~C~ 32 (347)
...|-|-+|-. +|.. .+...|+||.|+
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 34566666663 2311 124457777764
No 199
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=31.88 E-value=23 Score=23.50 Aligned_cols=11 Identities=45% Similarity=0.960 Sum_probs=7.6
Q ss_pred ccCCCCCCCce
Q 036250 26 IKCPFCETGFV 36 (347)
Q Consensus 26 ~~CP~C~sGFi 36 (347)
-.||+|..||-
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 35999999984
No 200
>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=31.76 E-value=22 Score=24.38 Aligned_cols=43 Identities=30% Similarity=0.566 Sum_probs=25.8
Q ss_pred cchhhhhhhccCCceEEecCCCcccccchHHHHh------cCCCCCCCC
Q 036250 215 QCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLE------LQSSCPICR 257 (347)
Q Consensus 215 ~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~------~~~~CP~CR 257 (347)
.|.||......+.-+.=-.|...||..|+..=+. ..-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 3788988443222222224899999999965442 123577764
No 201
>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=31.40 E-value=25 Score=29.09 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=17.9
Q ss_pred eecCCceeeecCCCCccCCCCCCCceEe
Q 036250 11 CYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
|-+|.-+..-..+..++||.|.--+-++
T Consensus 5 CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEecCCeeECcccccccccc
Confidence 6677776655555557777777666544
No 202
>PRK10220 hypothetical protein; Provisional
Probab=31.32 E-value=27 Score=28.93 Aligned_cols=28 Identities=18% Similarity=0.415 Sum_probs=21.0
Q ss_pred eecCCceeeecCCCCccCCCCCCCceEe
Q 036250 11 CYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
|-+|.-+..-..++.++||.|.--|-.+
T Consensus 6 CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 7888888765556568888888877655
No 203
>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=31.18 E-value=8.7 Score=36.91 Aligned_cols=45 Identities=20% Similarity=0.347 Sum_probs=20.6
Q ss_pred cccchhhhhhhccCCceEEe---cCCCcccccchHHHHhcCCCCCCCCc
Q 036250 213 DLQCAVCLEEFVMGNEAKEM---PCKHKFHGECIMPWLELQSSCPICRY 258 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~l---pC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (347)
...|+||-..-..+. ++.- --.|.+|.-|-..|-..+..||.|-.
T Consensus 172 ~g~CPvCGs~P~~s~-l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSV-LRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEE-EE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CCcCCCCCCcCceEE-EecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 468999988752210 0000 02466888899999888889999944
No 204
>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=30.42 E-value=39 Score=28.79 Aligned_cols=33 Identities=9% Similarity=0.024 Sum_probs=23.3
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEe
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQ 38 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE 38 (347)
..-+-|..|....-=+.-.-++||.|+.-|-.+
T Consensus 7 GtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CccccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 345669999776533333469999999988666
No 205
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.40 E-value=16 Score=21.92 Aligned_cols=13 Identities=31% Similarity=0.953 Sum_probs=10.2
Q ss_pred ccCCCCCCCceEe
Q 036250 26 IKCPFCETGFVEQ 38 (347)
Q Consensus 26 ~~CP~C~sGFiEE 38 (347)
+.||.|+-.|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 5699999999654
No 206
>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=30.31 E-value=27 Score=35.41 Aligned_cols=26 Identities=27% Similarity=0.581 Sum_probs=18.6
Q ss_pred eeecCCceeeec---CCCCccCCCCCCCc
Q 036250 10 WCYICSRMVNPR---MEAGIKCPFCETGF 35 (347)
Q Consensus 10 wCh~C~~~V~p~---~~~e~~CP~C~sGF 35 (347)
=||.|..-++.. .++...||||+.--
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 399999887422 23357899999854
No 207
>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=30.15 E-value=44 Score=21.60 Aligned_cols=28 Identities=14% Similarity=0.384 Sum_probs=18.6
Q ss_pred EeeecCCceeeec---C---CCCccCCCCCCCce
Q 036250 9 YWCYICSRMVNPR---M---EAGIKCPFCETGFV 36 (347)
Q Consensus 9 ywCh~C~~~V~p~---~---~~e~~CP~C~sGFi 36 (347)
+=|-.|...+... + +..+.||+|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4588888876533 1 12488999988664
No 208
>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=29.38 E-value=12 Score=22.48 Aligned_cols=11 Identities=45% Similarity=1.328 Sum_probs=9.0
Q ss_pred ccCCCCCCCce
Q 036250 26 IKCPFCETGFV 36 (347)
Q Consensus 26 ~~CP~C~sGFi 36 (347)
+.||.|+..|.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 88999988774
No 209
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=29.24 E-value=20 Score=26.68 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=10.5
Q ss_pred CCCCccCCCCCCCc
Q 036250 22 MEAGIKCPFCETGF 35 (347)
Q Consensus 22 ~~~e~~CP~C~sGF 35 (347)
+...++||.|+--|
T Consensus 50 ~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 50 VEGELICPECGREY 63 (68)
T ss_dssp TTTEEEETTTTEEE
T ss_pred cCCEEEcCCCCCEE
Confidence 44579999998655
No 210
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.21 E-value=52 Score=33.70 Aligned_cols=39 Identities=23% Similarity=0.556 Sum_probs=30.2
Q ss_pred CCCCCCCcEeeecCCceeeecCCCCccCCCCCC--CceEecCCCC
Q 036250 1 MGDATVGSYWCYICSRMVNPRMEAGIKCPFCET--GFVEQMSSSI 43 (347)
Q Consensus 1 m~~~~~~rywCh~C~~~V~p~~~~e~~CP~C~s--GFiEE~~~~~ 43 (347)
|+... .-|-|-.|--.-.-|++ +||.|+. -|+||.....
T Consensus 1 MaK~~-t~f~C~~CG~~s~KW~G---kCp~Cg~Wns~vE~~~~~~ 41 (456)
T COG1066 1 MAKKK-TAFVCQECGYVSPKWLG---KCPACGAWNTLVEEVLAAS 41 (456)
T ss_pred CCCcc-cEEEcccCCCCCccccc---cCCCCCCccceEEeecccc
Confidence 44444 66889999887776776 7999996 8999997554
No 211
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=29.14 E-value=26 Score=28.11 Aligned_cols=24 Identities=25% Similarity=0.746 Sum_probs=19.4
Q ss_pred eeecCCceeeecCCCCccCCCCCCC
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
||-.|...+.+.. ..++||.|+--
T Consensus 2 fC~~Cg~~l~~~~-~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN-GVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCC-CeEECcCCCCc
Confidence 8999999987653 37999999853
No 212
>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=28.71 E-value=33 Score=23.49 Aligned_cols=12 Identities=33% Similarity=0.977 Sum_probs=9.5
Q ss_pred CCCccCCCCCCC
Q 036250 23 EAGIKCPFCETG 34 (347)
Q Consensus 23 ~~e~~CP~C~sG 34 (347)
++.++||+|++-
T Consensus 16 ~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCCe
Confidence 345889999985
No 213
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=28.32 E-value=50 Score=35.55 Aligned_cols=44 Identities=18% Similarity=0.560 Sum_probs=24.9
Q ss_pred ccchhhhhhhccCCceEEecCCCcccc--cchHH-HHh-c---CC--CCCCCCcccCCCC
Q 036250 214 LQCAVCLEEFVMGNEAKEMPCKHKFHG--ECIMP-WLE-L---QS--SCPICRYQLPSDD 264 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~~~~lpC~H~Fh~--~Ci~~-Wl~-~---~~--~CP~CR~~l~~~~ 264 (347)
+.|+|+.-.+ .+||.+..|+ .|.+. |+. . .. .||+|.+...-+.
T Consensus 307 L~CPl~~~Rm-------~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~ 359 (636)
T KOG2169|consen 307 LNCPLSKMRM-------SLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEG 359 (636)
T ss_pred ecCCccccee-------ecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccc
Confidence 5788877665 4454444444 56533 332 1 22 3999988764443
No 214
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=28.11 E-value=40 Score=21.25 Aligned_cols=21 Identities=29% Similarity=0.787 Sum_probs=12.4
Q ss_pred cEeeecCCceeeecCCCCccCCCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
+.+|..|.. - ..|+||.|+.-
T Consensus 2 ~~~C~vC~~-~-----~kY~Cp~C~~~ 22 (30)
T PF04438_consen 2 RKLCSVCGN-P-----AKYRCPRCGAR 22 (30)
T ss_dssp -EEETSSSS-E-----ESEE-TTT--E
T ss_pred cCCCccCcC-C-----CEEECCCcCCc
Confidence 567888877 1 25999999753
No 215
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.06 E-value=18 Score=34.51 Aligned_cols=46 Identities=22% Similarity=0.466 Sum_probs=36.8
Q ss_pred ccchhhhhhhcc---CCceEEec--------CCCcccccchHHHHhcC-CCCCCCCcc
Q 036250 214 LQCAVCLEEFVM---GNEAKEMP--------CKHKFHGECIMPWLELQ-SSCPICRYQ 259 (347)
Q Consensus 214 ~~C~ICl~~~~~---~~~~~~lp--------C~H~Fh~~Ci~~Wl~~~-~~CP~CR~~ 259 (347)
..|.||...+.. ...++.+. |+|..|..|+..-+... -.||.|+..
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 469999999973 23466777 99999999999988655 479999875
No 216
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=27.95 E-value=24 Score=23.56 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=16.2
Q ss_pred eecCCceeeecCCCC---ccCCCCCCCceE
Q 036250 11 CYICSRMVNPRMEAG---IKCPFCETGFVE 37 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e---~~CP~C~sGFiE 37 (347)
|-.|........-.+ ..||.|+|-|+.
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIWFD 31 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEEcc
Confidence 566766543332112 459999988875
No 217
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.69 E-value=39 Score=32.15 Aligned_cols=52 Identities=21% Similarity=0.266 Sum_probs=36.2
Q ss_pred ccchhhhhhhccC-CceEEecCCCcccccchHHHHhcCCCCCCCCcccCCCCCcc
Q 036250 214 LQCAVCLEEFVMG-NEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPSDDLKV 267 (347)
Q Consensus 214 ~~C~ICl~~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~ 267 (347)
..|+|---+|... .-....+|||+|-..-+.+. ...+|++|...+..++..+
T Consensus 112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEe
Confidence 5799877666321 12445579999988777664 3678999999887776543
No 218
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.55 E-value=29 Score=24.53 Aligned_cols=13 Identities=38% Similarity=1.014 Sum_probs=10.0
Q ss_pred ccCCCCCCCceEe
Q 036250 26 IKCPFCETGFVEQ 38 (347)
Q Consensus 26 ~~CP~C~sGFiEE 38 (347)
-.||.|+++|+..
T Consensus 21 ~fCP~Cg~~~m~~ 33 (50)
T PRK00432 21 KFCPRCGSGFMAE 33 (50)
T ss_pred CcCcCCCcchhec
Confidence 3799999986554
No 219
>PRK13794 hypothetical protein; Provisional
Probab=26.94 E-value=34 Score=35.50 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=21.2
Q ss_pred CcEeeecCCceeeecCCCCccCCCCCCC-ceEecC
Q 036250 7 GSYWCYICSRMVNPRMEAGIKCPFCETG-FVEQMS 40 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~~~e~~CP~C~sG-FiEE~~ 40 (347)
.-|||-.|+.+|- . -+|..|+.. |--.|.
T Consensus 9 ~~~wc~~cn~p~~---~--~~c~~cg~~~~~~~~~ 38 (479)
T PRK13794 9 HLKWCDNCNVPVL---G--KKCAICGSETREVKVT 38 (479)
T ss_pred EEEEcCCCCCeec---C--CchhHhCCCeeEEecC
Confidence 4699999998874 2 459999995 444443
No 220
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=26.22 E-value=43 Score=33.60 Aligned_cols=30 Identities=30% Similarity=0.568 Sum_probs=20.6
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCc
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGF 35 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGF 35 (347)
.--|+|-.|-..+.-..+.+-.||+|++-|
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~ 267 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGKV 267 (380)
T ss_pred CcEEEcccccceecccccccccCCcccccc
Confidence 446999999844443334467899999844
No 221
>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=25.97 E-value=32 Score=26.28 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=5.7
Q ss_pred CcEeeecCCceee
Q 036250 7 GSYWCYICSRMVN 19 (347)
Q Consensus 7 ~rywCh~C~~~V~ 19 (347)
.+|.|-.|.+.+.
T Consensus 16 ~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 16 GHYHCEACQKDYK 28 (70)
T ss_dssp TEEEETTT--EEE
T ss_pred CEEECccccccce
Confidence 3555555555544
No 222
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.92 E-value=42 Score=36.73 Aligned_cols=32 Identities=19% Similarity=0.534 Sum_probs=23.2
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCCCceEecCC
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCETGFVEQMSS 41 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~sGFiEE~~~ 41 (347)
.+...||.|...-. .+ ..||.|+|-=|..+..
T Consensus 460 ~~~L~CH~Cg~~~~--~p--~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 460 TGQLRCHYCGYQEP--IP--QSCPECGSEHLRAVGP 491 (730)
T ss_pred CCeeEeCCCCCCCC--CC--CCCCCCCCCeeEEecc
Confidence 35678999999843 23 6799999986665543
No 223
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=25.74 E-value=39 Score=34.45 Aligned_cols=23 Identities=26% Similarity=0.571 Sum_probs=16.9
Q ss_pred eeecCCceeeecCCCCccCCCCCCCc
Q 036250 10 WCYICSRMVNPRMEAGIKCPFCETGF 35 (347)
Q Consensus 10 wCh~C~~~V~p~~~~e~~CP~C~sGF 35 (347)
-||.|..-+. .....||||+.--
T Consensus 223 ~C~~Cd~l~~---~~~a~CpRC~~~L 245 (419)
T PRK15103 223 SCSCCTAILP---ADQPVCPRCHTKG 245 (419)
T ss_pred cCCCCCCCCC---CCCCCCCCCCCcC
Confidence 4999999652 2356899999864
No 224
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.24 E-value=35 Score=25.10 Aligned_cols=23 Identities=26% Similarity=0.547 Sum_probs=14.6
Q ss_pred eeecCCceeee-cCCCCccCCCCC
Q 036250 10 WCYICSRMVNP-RMEAGIKCPFCE 32 (347)
Q Consensus 10 wCh~C~~~V~p-~~~~e~~CP~C~ 32 (347)
-|+.|-..+.- .....++||.|+
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCG 53 (69)
T ss_pred CccCcccccccccccceEEcCCCC
Confidence 37777777654 223357788874
No 225
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.20 E-value=61 Score=27.01 Aligned_cols=43 Identities=26% Similarity=0.403 Sum_probs=29.8
Q ss_pred cchhhhhhhccC----------CceEEe-cCCCcccccchHHHHhcCCCCCCCC
Q 036250 215 QCAVCLEEFVMG----------NEAKEM-PCKHKFHGECIMPWLELQSSCPICR 257 (347)
Q Consensus 215 ~C~ICl~~~~~~----------~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (347)
.|--|+..|... .....- .|++.||.+|=.-+-+.-..||-|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 588888777421 111223 3999999999877777777799995
No 226
>PHA02776 E7 protein; Provisional
Probab=25.01 E-value=31 Score=28.23 Aligned_cols=27 Identities=26% Similarity=0.648 Sum_probs=19.9
Q ss_pred CcEe----eecCCceeeecC---------------C-CCccCCCCCC
Q 036250 7 GSYW----CYICSRMVNPRM---------------E-AGIKCPFCET 33 (347)
Q Consensus 7 ~ryw----Ch~C~~~V~p~~---------------~-~e~~CP~C~s 33 (347)
..|. |+.|.+.|+... + =.++||.|..
T Consensus 53 ~~Y~Ivt~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~ 99 (101)
T PHA02776 53 QAFQIVTCCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAP 99 (101)
T ss_pred CCeEEEeECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCC
Confidence 4676 999999997653 1 1489999964
No 227
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.00 E-value=25 Score=36.01 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=26.9
Q ss_pred ccchhhhhhhccCCc-----eEEecCCCcccccchHHHHhcC
Q 036250 214 LQCAVCLEEFVMGNE-----AKEMPCKHKFHGECIMPWLELQ 250 (347)
Q Consensus 214 ~~C~ICl~~~~~~~~-----~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (347)
..|+.|....+.... ....+|+|.||+.|+..|....
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 359999998865442 2223599999999988887553
No 228
>PF00527 E7: E7 protein, Early protein; InterPro: IPR000148 This family includes the E7 oncoprotein from various papillomaviruses []. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2F8B_A 2EWL_A 2B9D_A.
Probab=24.60 E-value=30 Score=27.65 Aligned_cols=25 Identities=24% Similarity=0.658 Sum_probs=14.5
Q ss_pred CcEe----eecCCceeeecC---------------C-CCccCCCC
Q 036250 7 GSYW----CYICSRMVNPRM---------------E-AGIKCPFC 31 (347)
Q Consensus 7 ~ryw----Ch~C~~~V~p~~---------------~-~e~~CP~C 31 (347)
..|+ |+.|.+.|+... + =.++||.|
T Consensus 47 ~~Y~V~t~C~~C~~~lrl~V~as~~~Ir~lq~LLl~~L~lvCp~C 91 (92)
T PF00527_consen 47 QPYRVVTCCGRCGKRLRLVVVASHEGIRTLQQLLLGDLSLVCPPC 91 (92)
T ss_dssp CEEEEEEEBTTT--EEEEEEEC-HHHHHHHHHHHHCT-EE--CCC
T ss_pred CCeEEEeECCCCCCEEEEEEEeChhhHHHHHHHhhcCceEeCCCC
Confidence 4565 999999997653 1 15889998
No 229
>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=24.29 E-value=25 Score=19.48 Aligned_cols=10 Identities=40% Similarity=1.358 Sum_probs=5.1
Q ss_pred ccCCCCCCCc
Q 036250 26 IKCPFCETGF 35 (347)
Q Consensus 26 ~~CP~C~sGF 35 (347)
++|+.|+..|
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 3577777655
No 230
>PHA00626 hypothetical protein
Probab=24.14 E-value=59 Score=23.80 Aligned_cols=29 Identities=14% Similarity=0.261 Sum_probs=18.0
Q ss_pred eecCCc-eeee-----cCCCCccCCCCCCCceEec
Q 036250 11 CYICSR-MVNP-----RMEAGIKCPFCETGFVEQM 39 (347)
Q Consensus 11 Ch~C~~-~V~p-----~~~~e~~CP~C~sGFiEE~ 39 (347)
|-.|.. .|.- .....|+||.|+--|-...
T Consensus 3 CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 3 CPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 666766 3432 1134799999988776543
No 231
>PLN02189 cellulose synthase
Probab=24.07 E-value=72 Score=36.19 Aligned_cols=48 Identities=19% Similarity=0.386 Sum_probs=31.9
Q ss_pred ccchhhhhhhccCC--ceE-Eec-CCCcccccchHHH-HhcCCCCCCCCcccC
Q 036250 214 LQCAVCLEEFVMGN--EAK-EMP-CKHKFHGECIMPW-LELQSSCPICRYQLP 261 (347)
Q Consensus 214 ~~C~ICl~~~~~~~--~~~-~lp-C~H~Fh~~Ci~~W-l~~~~~CP~CR~~l~ 261 (347)
..|.||-+++.... ++. --. |+--.|..|..-= -+.++.||-|+....
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 37999999985322 222 222 7777899998322 234668999988765
No 232
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=23.97 E-value=35 Score=24.43 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=19.2
Q ss_pred CcEeeecCCceeeecC----CCCccCCCC
Q 036250 7 GSYWCYICSRMVNPRM----EAGIKCPFC 31 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~----~~e~~CP~C 31 (347)
.|-|||-|...--|+. =.|.+|--|
T Consensus 2 ~Rq~CyLCdlPr~PWami~df~EpVCRgC 30 (54)
T PF11261_consen 2 RRQQCYLCDLPRMPWAMIWDFSEPVCRGC 30 (54)
T ss_pred CceeEEeccCCCCchHHHhhccchhhhhh
Confidence 5889999999888875 136777766
No 233
>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=23.82 E-value=26 Score=35.33 Aligned_cols=28 Identities=21% Similarity=0.404 Sum_probs=0.0
Q ss_pred ecCCCcccccchHHHHhc---CCCCCCCCcc
Q 036250 232 MPCKHKFHGECIMPWLEL---QSSCPICRYQ 259 (347)
Q Consensus 232 lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR~~ 259 (347)
|.|+|++...=...-.+. ...||+||..
T Consensus 307 l~CGHVhG~h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 307 LNCGHVHGYHNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp -------------------------------
T ss_pred ccccceeeecccccccccccccccCCCcccc
No 234
>PF12773 DZR: Double zinc ribbon
Probab=23.81 E-value=39 Score=23.17 Aligned_cols=26 Identities=23% Similarity=0.609 Sum_probs=13.5
Q ss_pred cEeeecCCceeeecCCCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
.-||..|-..+.......++||.|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcC
Confidence 34566666666522222356666665
No 235
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=23.69 E-value=56 Score=32.08 Aligned_cols=48 Identities=6% Similarity=-0.089 Sum_probs=35.7
Q ss_pred ccccccccchhhhhhhccCCceEEecCCCc-ccccchHHHHhcCCCCCCCCccc
Q 036250 208 VAIDQDLQCAVCLEEFVMGNEAKEMPCKHK-FHGECIMPWLELQSSCPICRYQL 260 (347)
Q Consensus 208 ~~~~~~~~C~ICl~~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (347)
..+...++|-+|-+-+ -.....+|+|. ||-.|.. +....+||+|....
T Consensus 338 ~~~~s~~~~~~~~~~~---~st~~~~~~~n~~~~~~a~--~s~~~~~~~c~~~~ 386 (394)
T KOG2113|consen 338 NGLMSSLKGTSAGFGL---LSTIWSGGNMNLSPGSLAS--ASASPTSSTCDHND 386 (394)
T ss_pred ccchhhcccccccCce---eeeEeecCCcccChhhhhh--cccCCccccccccc
Confidence 3344457899998887 55678889986 8888876 56677899997643
No 236
>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=23.27 E-value=48 Score=21.99 Aligned_cols=24 Identities=21% Similarity=0.848 Sum_probs=18.3
Q ss_pred cEeeecCCceeeecCCCCccCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCE 32 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~ 32 (347)
.-||..|...|.-.. ..++|+.|+
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~~C~ 34 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCSWCK 34 (49)
T ss_pred CCCccccccccCcCC-CCcCCCCCC
Confidence 458999999986433 368999984
No 237
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.23 E-value=45 Score=27.80 Aligned_cols=21 Identities=33% Similarity=1.056 Sum_probs=16.8
Q ss_pred EeeecCCceeeecCCCCccCCCCC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCE 32 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~ 32 (347)
|+|-+|...|- .+| +.||-|+
T Consensus 2 Y~CPrC~skvC-~LP--~~CpiCg 22 (112)
T TIGR00622 2 YFCPQCRAKVC-ELP--VECPICG 22 (112)
T ss_pred ccCCCCCCCcc-CCC--CcCCcCC
Confidence 88999998885 566 7799884
No 238
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.09 E-value=30 Score=21.42 Aligned_cols=23 Identities=17% Similarity=0.576 Sum_probs=9.2
Q ss_pred EeeecCCceeeecCCCCccCCCCCC
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
+.|..|.+.+.. ..-|.|+.|+-
T Consensus 1 ~~C~~C~~~~~~--~~~Y~C~~Cdf 23 (30)
T PF07649_consen 1 FRCDACGKPIDG--GWFYRCSECDF 23 (30)
T ss_dssp ---TTTS----S----EEE-TTT--
T ss_pred CcCCcCCCcCCC--CceEECccCCC
Confidence 578999998874 22588999964
No 239
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=23.00 E-value=33 Score=24.85 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=16.0
Q ss_pred cEeeecCCceeeecC---CCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPRM---EAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~~---~~e~~CP~C~s 33 (347)
.--|-.|..-.--.- --|++||+|--
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccce
Confidence 345777776553221 22799999964
No 240
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=22.85 E-value=81 Score=20.70 Aligned_cols=30 Identities=20% Similarity=0.434 Sum_probs=22.1
Q ss_pred cEeeecCCceeeecC---CCCccCCCCCCCceE
Q 036250 8 SYWCYICSRMVNPRM---EAGIKCPFCETGFVE 37 (347)
Q Consensus 8 rywCh~C~~~V~p~~---~~e~~CP~C~sGFiE 37 (347)
|.-|-.|.+...... ..+-+|..|++.+|.
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred CcCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 567889998876442 236889999997764
No 241
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=22.82 E-value=37 Score=34.29 Aligned_cols=24 Identities=25% Similarity=0.618 Sum_probs=18.6
Q ss_pred cEeeecCCceeeecCCCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~s 33 (347)
---||.|...-... ++..||+|++
T Consensus 220 ~~~C~~C~~~~~~~--~~~~CpRC~~ 243 (418)
T COG2995 220 LRSCLCCHYILPHD--AEPRCPRCGS 243 (418)
T ss_pred ceecccccccCCHh--hCCCCCCCCC
Confidence 34599998876543 5799999997
No 242
>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=22.39 E-value=35 Score=21.67 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=8.7
Q ss_pred eecCCceeeecCCCCccCCCCCC
Q 036250 11 CYICSRMVNPRMEAGIKCPFCET 33 (347)
Q Consensus 11 Ch~C~~~V~p~~~~e~~CP~C~s 33 (347)
|-.|.-+..-.-..-++||.|..
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp -TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCcceeccCCEEeCCcccc
Confidence 55555555433333466777753
No 243
>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=22.28 E-value=32 Score=24.33 Aligned_cols=12 Identities=33% Similarity=1.018 Sum_probs=6.0
Q ss_pred CCCCCCcccCCC
Q 036250 252 SCPICRYQLPSD 263 (347)
Q Consensus 252 ~CP~CR~~l~~~ 263 (347)
.||+|.++|..+
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799998887543
No 244
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=21.98 E-value=33 Score=33.56 Aligned_cols=26 Identities=19% Similarity=0.579 Sum_probs=17.1
Q ss_pred cEeeecCCceeeec----------------CCCCccCCCCCC
Q 036250 8 SYWCYICSRMVNPR----------------MEAGIKCPFCET 33 (347)
Q Consensus 8 rywCh~C~~~V~p~----------------~~~e~~CP~C~s 33 (347)
-+||-+|...|-+. ++.+-+||.|+.
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d 131 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDD 131 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhcCccccCcCccc
Confidence 46777777666432 233568999986
No 245
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.95 E-value=59 Score=26.75 Aligned_cols=18 Identities=28% Similarity=0.606 Sum_probs=12.5
Q ss_pred eeecCCCCccCCCCCCCce
Q 036250 18 VNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 18 V~p~~~~e~~CP~C~sGFi 36 (347)
|..-++ ...||.|+..|=
T Consensus 43 V~ie~G-~t~CP~Cg~~~e 60 (115)
T COG1885 43 VEIEVG-STSCPKCGEPFE 60 (115)
T ss_pred EEEecc-cccCCCCCCccc
Confidence 444445 688999998763
No 246
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.87 E-value=69 Score=32.83 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=25.4
Q ss_pred CCcEeeecCCceeeecCCCCccCCCCCC--CceEec
Q 036250 6 VGSYWCYICSRMVNPRMEAGIKCPFCET--GFVEQM 39 (347)
Q Consensus 6 ~~rywCh~C~~~V~p~~~~e~~CP~C~s--GFiEE~ 39 (347)
-..|-|..|--.-.-|.. .||.|+. .|+||+
T Consensus 5 ~~~y~C~~Cg~~~~~~~g---~Cp~C~~w~t~~e~~ 37 (446)
T PRK11823 5 KTAYVCQECGAESPKWLG---RCPECGAWNTLVEEV 37 (446)
T ss_pred CCeEECCcCCCCCcccCe---eCcCCCCccceeeec
Confidence 467999999988776654 6999997 788876
No 247
>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=21.82 E-value=53 Score=28.53 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=14.4
Q ss_pred CccCCCCCCCceEecCC
Q 036250 25 GIKCPFCETGFVEQMSS 41 (347)
Q Consensus 25 e~~CP~C~sGFiEE~~~ 41 (347)
.+.||+|+|...+++..
T Consensus 105 ~~~cp~c~s~~t~~~s~ 121 (146)
T TIGR02159 105 SVQCPRCGSADTTITSI 121 (146)
T ss_pred CCcCCCCCCCCcEeecC
Confidence 48899999999988763
No 248
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.75 E-value=99 Score=30.23 Aligned_cols=48 Identities=21% Similarity=0.529 Sum_probs=36.6
Q ss_pred cccchhhhhhhccCCceEEecCCCcccccchHHHHhcCCCCCCCCcccCC
Q 036250 213 DLQCAVCLEEFVMGNEAKEMPCKHKFHGECIMPWLELQSSCPICRYQLPS 262 (347)
Q Consensus 213 ~~~C~ICl~~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (347)
...|-||...+.... +.--|.|.|+..|...|......||.|+.....
T Consensus 105 ~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~p 152 (324)
T KOG0824|consen 105 HDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKISP 152 (324)
T ss_pred ccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCcCc
Confidence 357889988884221 122299999999999999999999999876533
No 249
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.74 E-value=44 Score=24.90 Aligned_cols=9 Identities=33% Similarity=1.191 Sum_probs=7.4
Q ss_pred CccCCCCCC
Q 036250 25 GIKCPFCET 33 (347)
Q Consensus 25 e~~CP~C~s 33 (347)
-+.||+|+|
T Consensus 5 ~~~CPRC~S 13 (63)
T PF02701_consen 5 PLPCPRCDS 13 (63)
T ss_pred CCCCCCcCC
Confidence 478999987
No 250
>PRK00420 hypothetical protein; Validated
Probab=21.68 E-value=56 Score=27.20 Aligned_cols=27 Identities=15% Similarity=0.412 Sum_probs=19.5
Q ss_pred EeeecCCceeeecCCCCccCCCCCCCc
Q 036250 9 YWCYICSRMVNPRMEAGIKCPFCETGF 35 (347)
Q Consensus 9 ywCh~C~~~V~p~~~~e~~CP~C~sGF 35 (347)
.-|-.|.-+.--....++.||.|+.-.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCee
Confidence 458889977754234589999999833
No 251
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.57 E-value=42 Score=28.91 Aligned_cols=52 Identities=23% Similarity=0.512 Sum_probs=26.7
Q ss_pred ccccccccchhhhhh-hccCCceEEecCCCcccccchHHHHhcCC----CCCCCCcc
Q 036250 208 VAIDQDLQCAVCLEE-FVMGNEAKEMPCKHKFHGECIMPWLELQS----SCPICRYQ 259 (347)
Q Consensus 208 ~~~~~~~~C~ICl~~-~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~ 259 (347)
+.+..+.+|-||+.. |.+|.--.-.-|.-.||..|--+--.+.+ .|-+|+..
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 344567799999875 33332222222444445555433222222 38888775
No 252
>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=21.33 E-value=54 Score=23.70 Aligned_cols=30 Identities=13% Similarity=0.348 Sum_probs=21.3
Q ss_pred cEeeecCCceeeec---CCCCccCCCCCCCceE
Q 036250 8 SYWCYICSRMVNPR---MEAGIKCPFCETGFVE 37 (347)
Q Consensus 8 rywCh~C~~~V~p~---~~~e~~CP~C~sGFiE 37 (347)
.|-|-.|-..|... ++..+.||.|+.-|--
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 35699999998543 2345789999887643
No 253
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=21.17 E-value=54 Score=33.44 Aligned_cols=26 Identities=27% Similarity=0.620 Sum_probs=18.2
Q ss_pred eeecCCceeeec-C--CCCccCCCCCCCc
Q 036250 10 WCYICSRMVNPR-M--EAGIKCPFCETGF 35 (347)
Q Consensus 10 wCh~C~~~V~p~-~--~~e~~CP~C~sGF 35 (347)
=||.|..-+... + +....||||+.--
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 399999887422 2 2236799999854
No 254
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=21.09 E-value=79 Score=31.74 Aligned_cols=30 Identities=23% Similarity=0.434 Sum_probs=20.1
Q ss_pred CcEeeecCCceeeecCCCCccCCCCCCCce
Q 036250 7 GSYWCYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
--|.|+.|........+..-.||.|++-|+
T Consensus 243 ~~~~C~~c~~~~~~~~~~~~~C~~c~~~~~ 272 (382)
T PRK04338 243 YVYYCPKCLYREEVEGLPPEECPVCGGKFG 272 (382)
T ss_pred eEEECCCCCcEEEecCCCCCCCCCCCCcce
Confidence 368899998875322222457999987554
No 255
>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=20.72 E-value=56 Score=23.05 Aligned_cols=27 Identities=30% Similarity=0.857 Sum_probs=14.8
Q ss_pred Eeeec--CCceeeecCCC-C--ccCCCCCCCc
Q 036250 9 YWCYI--CSRMVNPRMEA-G--IKCPFCETGF 35 (347)
Q Consensus 9 ywCh~--C~~~V~p~~~~-e--~~CP~C~sGF 35 (347)
-||-. |...|...... . ++||.|+.-|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 39988 99998755432 2 7899998766
No 256
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.56 E-value=52 Score=28.17 Aligned_cols=29 Identities=21% Similarity=0.445 Sum_probs=21.5
Q ss_pred CcEeeecCCceeeecCCCCccCCCCCCCce
Q 036250 7 GSYWCYICSRMVNPRMEAGIKCPFCETGFV 36 (347)
Q Consensus 7 ~rywCh~C~~~V~p~~~~e~~CP~C~sGFi 36 (347)
.-+-|-.|-...--. ..+++||.|+--++
T Consensus 27 L~~hCp~Cg~PLF~K-dG~v~CPvC~~~~~ 55 (131)
T COG1645 27 LAKHCPKCGTPLFRK-DGEVFCPVCGYREV 55 (131)
T ss_pred HHhhCcccCCcceee-CCeEECCCCCceEE
Confidence 346799999887544 44899999996443
No 257
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.32 E-value=65 Score=25.14 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=18.1
Q ss_pred ccchhhhhhhccCC--ceEE--ecCCCcccccchHHHH-hcCCCCCCCCcccC
Q 036250 214 LQCAVCLEEFVMGN--EAKE--MPCKHKFHGECIMPWL-ELQSSCPICRYQLP 261 (347)
Q Consensus 214 ~~C~ICl~~~~~~~--~~~~--lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~ 261 (347)
..|.||-+.+.... ++.. .-|+--.|..|..-=. +.+..||-|+....
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 47999999985432 2222 2377777888874333 45678999986553
No 258
>PRK06260 threonine synthase; Validated
Probab=20.15 E-value=70 Score=32.06 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=19.9
Q ss_pred cEeeecCCceeeecCCCCccCCCCCCC
Q 036250 8 SYWCYICSRMVNPRMEAGIKCPFCETG 34 (347)
Q Consensus 8 rywCh~C~~~V~p~~~~e~~CP~C~sG 34 (347)
.|-|..|-++..+... .+.||.|++-
T Consensus 3 ~~~C~~cg~~~~~~~~-~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDPDEI-IYTCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCCCCc-cccCCCCCCe
Confidence 5889999999864432 5889999753
Done!