Query 017955
Match_columns 363
No_of_seqs 260 out of 1734
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:53:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017955.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017955hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13639 zf-RING_2: Ring finge 99.5 6.6E-15 1.4E-19 103.3 2.2 43 283-325 2-44 (44)
2 KOG4628 Predicted E3 ubiquitin 99.5 2E-14 4.2E-19 141.0 4.9 77 258-334 203-283 (348)
3 PF14369 zf-RING_3: zinc-finge 99.4 7.7E-14 1.7E-18 93.4 2.2 34 23-57 2-35 (35)
4 PHA02929 N1R/p28-like protein; 99.2 1.2E-11 2.7E-16 116.4 6.3 68 262-329 150-227 (238)
5 PF12678 zf-rbx1: RING-H2 zinc 99.2 8.7E-12 1.9E-16 97.1 3.8 46 280-325 18-73 (73)
6 COG5243 HRD1 HRD ubiquitin lig 99.2 1.3E-11 2.8E-16 120.4 4.0 68 262-329 267-345 (491)
7 COG5540 RING-finger-containing 99.1 2.3E-11 5E-16 116.1 3.9 51 280-330 322-373 (374)
8 KOG0317 Predicted E3 ubiquitin 99.1 5E-11 1.1E-15 113.4 2.2 51 280-333 238-288 (293)
9 PF13920 zf-C3HC4_3: Zinc fing 99.0 1.8E-10 4E-15 82.9 3.4 46 281-329 2-48 (50)
10 PLN03208 E3 ubiquitin-protein 99.0 2.4E-10 5.3E-15 103.9 4.6 55 280-337 17-87 (193)
11 PF13923 zf-C3HC4_2: Zinc fing 99.0 4.2E-10 9.2E-15 76.9 3.0 39 284-324 1-39 (39)
12 cd00162 RING RING-finger (Real 98.9 6.8E-10 1.5E-14 76.1 3.7 44 283-328 1-45 (45)
13 smart00504 Ubox Modified RING 98.9 1.2E-09 2.6E-14 81.6 4.2 52 282-336 2-53 (63)
14 PF15227 zf-C3HC4_4: zinc fing 98.9 1.4E-09 3E-14 75.8 3.3 38 284-324 1-42 (42)
15 KOG0823 Predicted E3 ubiquitin 98.8 7.7E-10 1.7E-14 102.5 1.4 50 280-332 46-98 (230)
16 KOG0320 Predicted E3 ubiquitin 98.8 1.3E-09 2.9E-14 97.2 2.8 51 280-331 130-180 (187)
17 PHA02926 zinc finger-like prot 98.8 2.2E-09 4.7E-14 99.1 3.2 52 280-331 169-232 (242)
18 KOG0802 E3 ubiquitin ligase [P 98.8 1.7E-09 3.7E-14 113.4 2.1 49 280-328 290-340 (543)
19 PF12861 zf-Apc11: Anaphase-pr 98.8 3.7E-09 8E-14 84.2 3.3 51 280-330 20-83 (85)
20 PF14634 zf-RING_5: zinc-RING 98.7 6.5E-09 1.4E-13 73.0 3.1 44 283-326 1-44 (44)
21 PF00097 zf-C3HC4: Zinc finger 98.7 6.5E-09 1.4E-13 71.4 3.0 39 284-324 1-41 (41)
22 smart00184 RING Ring finger. E 98.7 1.1E-08 2.3E-13 67.7 3.4 38 284-324 1-39 (39)
23 TIGR00599 rad18 DNA repair pro 98.6 1.6E-08 3.5E-13 101.7 3.8 50 279-331 24-73 (397)
24 COG5194 APC11 Component of SCF 98.6 1.7E-08 3.7E-13 78.8 2.8 51 281-331 20-83 (88)
25 COG5574 PEX10 RING-finger-cont 98.5 4.2E-08 9E-13 92.6 2.2 50 280-332 214-265 (271)
26 KOG0287 Postreplication repair 98.5 4.5E-08 9.7E-13 95.1 1.6 51 280-333 22-72 (442)
27 PF04564 U-box: U-box domain; 98.5 1E-07 2.2E-12 74.1 3.0 54 281-337 4-58 (73)
28 KOG2164 Predicted E3 ubiquitin 98.4 9E-08 2E-12 97.5 2.5 49 281-332 186-239 (513)
29 PF13445 zf-RING_UBOX: RING-ty 98.4 2E-07 4.2E-12 65.4 2.8 38 284-322 1-43 (43)
30 KOG1493 Anaphase-promoting com 98.3 1.9E-07 4.2E-12 72.4 0.6 50 280-329 19-81 (84)
31 smart00744 RINGv The RING-vari 98.3 6.7E-07 1.5E-11 64.4 3.2 42 283-325 1-49 (49)
32 COG5432 RAD18 RING-finger-cont 98.3 3.4E-07 7.3E-12 87.4 2.0 47 280-329 24-70 (391)
33 KOG0828 Predicted E3 ubiquitin 98.2 5.1E-07 1.1E-11 91.4 1.6 50 281-330 571-635 (636)
34 COG5219 Uncharacterized conser 98.2 7.5E-07 1.6E-11 95.7 2.6 52 278-329 1466-1523(1525)
35 KOG4445 Uncharacterized conser 98.1 1.1E-06 2.4E-11 84.4 2.1 95 237-332 72-189 (368)
36 TIGR00570 cdk7 CDK-activating 98.1 2E-06 4.3E-11 83.8 3.6 52 281-332 3-57 (309)
37 KOG1734 Predicted RING-contain 98.1 8.1E-07 1.8E-11 84.1 0.5 50 280-329 223-281 (328)
38 KOG2930 SCF ubiquitin ligase, 98.1 2.6E-06 5.6E-11 69.8 2.9 49 280-328 45-107 (114)
39 KOG2177 Predicted E3 ubiquitin 98.1 1.4E-06 3.1E-11 81.1 1.5 44 280-326 12-55 (386)
40 PF11793 FANCL_C: FANCL C-term 98.0 5.8E-07 1.3E-11 69.4 -1.0 49 281-329 2-66 (70)
41 KOG0825 PHD Zn-finger protein 98.0 9.7E-07 2.1E-11 93.4 -0.2 51 280-330 122-172 (1134)
42 KOG0824 Predicted E3 ubiquitin 97.9 3.2E-06 7E-11 81.3 1.6 49 281-332 7-56 (324)
43 KOG1039 Predicted E3 ubiquitin 97.9 6.9E-06 1.5E-10 81.4 2.3 54 279-332 159-224 (344)
44 KOG0311 Predicted E3 ubiquitin 97.8 2.7E-06 5.9E-11 83.3 -1.5 49 280-330 42-91 (381)
45 KOG4265 Predicted E3 ubiquitin 97.8 1.3E-05 2.9E-10 78.8 3.1 48 280-330 289-337 (349)
46 KOG3970 Predicted E3 ubiquitin 97.8 2.2E-05 4.8E-10 72.8 4.2 73 280-353 49-133 (299)
47 PF14835 zf-RING_6: zf-RING of 97.7 9.5E-06 2.1E-10 61.3 -0.2 49 281-333 7-55 (65)
48 KOG0827 Predicted E3 ubiquitin 97.6 2.1E-05 4.5E-10 78.0 2.0 47 283-329 6-56 (465)
49 KOG0804 Cytoplasmic Zn-finger 97.6 2.2E-05 4.7E-10 79.2 1.5 48 280-329 174-222 (493)
50 KOG1785 Tyrosine kinase negati 97.5 2.4E-05 5.3E-10 77.8 0.7 51 282-335 370-422 (563)
51 KOG1645 RING-finger-containing 97.4 8.4E-05 1.8E-09 74.2 3.2 49 281-329 4-56 (463)
52 KOG0978 E3 ubiquitin ligase in 97.3 6.7E-05 1.5E-09 80.0 0.8 50 280-332 642-692 (698)
53 KOG2660 Locus-specific chromos 97.3 5.8E-05 1.3E-09 73.6 -0.0 53 277-331 11-63 (331)
54 KOG4159 Predicted E3 ubiquitin 97.1 0.00028 6.1E-09 71.4 3.2 50 280-332 83-132 (398)
55 PF11789 zf-Nse: Zinc-finger o 97.1 0.0003 6.5E-09 52.2 2.0 42 280-323 10-53 (57)
56 KOG0297 TNF receptor-associate 97.1 0.00021 4.6E-09 72.4 1.5 52 280-334 20-72 (391)
57 KOG1941 Acetylcholine receptor 97.0 0.0002 4.3E-09 71.3 0.7 47 280-326 364-413 (518)
58 KOG4172 Predicted E3 ubiquitin 97.0 0.00014 3.1E-09 53.1 -0.5 46 282-330 8-55 (62)
59 COG5152 Uncharacterized conser 96.7 0.00084 1.8E-08 61.4 2.3 51 281-334 196-246 (259)
60 KOG1813 Predicted E3 ubiquitin 96.5 0.0012 2.7E-08 63.7 2.0 54 282-338 242-295 (313)
61 KOG1428 Inhibitor of type V ad 96.5 0.0015 3.3E-08 73.5 2.7 52 280-331 3485-3546(3738)
62 KOG1814 Predicted E3 ubiquitin 96.4 0.0015 3.2E-08 65.6 1.9 46 281-326 184-237 (445)
63 PF12906 RINGv: RING-variant d 96.4 0.0023 4.9E-08 45.6 2.3 40 284-324 1-47 (47)
64 PF04641 Rtf2: Rtf2 RING-finge 96.3 0.0078 1.7E-07 57.7 5.9 91 241-332 58-164 (260)
65 KOG2879 Predicted E3 ubiquitin 96.2 0.0044 9.5E-08 59.4 3.7 49 279-329 237-287 (298)
66 KOG1002 Nucleotide excision re 96.2 0.0021 4.6E-08 66.3 1.5 56 280-338 535-595 (791)
67 PF14570 zf-RING_4: RING/Ubox 96.1 0.0033 7.2E-08 45.1 1.9 45 284-328 1-47 (48)
68 PHA03096 p28-like protein; Pro 96.0 0.003 6.6E-08 61.4 1.8 45 282-326 179-231 (284)
69 COG5222 Uncharacterized conser 95.9 0.0043 9.3E-08 60.1 2.2 42 282-326 275-318 (427)
70 KOG4692 Predicted E3 ubiquitin 95.9 0.0039 8.4E-08 61.6 1.8 49 280-331 421-469 (489)
71 KOG1571 Predicted E3 ubiquitin 95.8 0.0032 7E-08 62.3 0.9 46 280-331 304-349 (355)
72 KOG1952 Transcription factor N 95.8 0.0052 1.1E-07 66.6 2.3 70 280-349 190-267 (950)
73 PF10446 DUF2457: Protein of u 95.6 0.0041 8.8E-08 63.2 0.7 10 244-253 209-218 (458)
74 PHA02862 5L protein; Provision 95.6 0.0086 1.9E-07 52.4 2.6 45 282-330 3-54 (156)
75 PF05883 Baculo_RING: Baculovi 95.6 0.0074 1.6E-07 52.2 2.2 44 281-324 26-75 (134)
76 KOG0801 Predicted E3 ubiquitin 95.5 0.0041 8.9E-08 55.3 0.4 29 280-308 176-204 (205)
77 COG5236 Uncharacterized conser 95.5 0.011 2.5E-07 58.3 3.3 46 280-328 60-107 (493)
78 KOG4185 Predicted E3 ubiquitin 95.5 0.014 3.1E-07 56.5 4.0 51 282-332 4-58 (296)
79 KOG4275 Predicted E3 ubiquitin 95.3 0.0032 6.9E-08 60.8 -1.2 41 281-328 300-341 (350)
80 PHA02825 LAP/PHD finger-like p 95.2 0.013 2.9E-07 52.0 2.6 48 280-331 7-61 (162)
81 KOG3039 Uncharacterized conser 95.2 0.018 4E-07 54.5 3.6 58 280-337 220-278 (303)
82 PF10367 Vps39_2: Vacuolar sor 95.2 0.0088 1.9E-07 48.7 1.3 32 280-312 77-108 (109)
83 KOG0826 Predicted E3 ubiquitin 95.2 0.02 4.3E-07 56.2 3.9 46 280-328 299-345 (357)
84 PF14447 Prok-RING_4: Prokaryo 95.0 0.013 2.7E-07 43.2 1.4 47 282-333 8-54 (55)
85 KOG1832 HIV-1 Vpr-binding prot 94.9 0.022 4.7E-07 62.4 3.5 13 41-53 1326-1338(1516)
86 KOG1940 Zn-finger protein [Gen 94.8 0.019 4.1E-07 55.6 2.5 57 281-338 158-215 (276)
87 KOG4739 Uncharacterized protei 94.7 0.01 2.2E-07 56.0 0.5 46 282-330 4-49 (233)
88 KOG0827 Predicted E3 ubiquitin 94.7 0.0031 6.8E-08 62.9 -3.1 57 281-337 196-253 (465)
89 PF04931 DNA_pol_phi: DNA poly 94.7 0.024 5.3E-07 62.4 3.4 7 239-245 731-737 (784)
90 COG0375 HybF Zn finger protein 94.5 0.026 5.6E-07 47.8 2.5 35 20-58 67-101 (115)
91 PF10272 Tmpp129: Putative tra 94.5 0.044 9.6E-07 55.0 4.6 69 264-332 253-354 (358)
92 COG5175 MOT2 Transcriptional r 94.5 0.019 4.1E-07 56.6 1.8 56 278-333 11-68 (480)
93 PF08746 zf-RING-like: RING-li 94.3 0.018 3.9E-07 40.3 0.9 41 284-324 1-43 (43)
94 PF10446 DUF2457: Protein of u 94.3 0.015 3.3E-07 59.1 0.6 6 117-122 38-43 (458)
95 PF03854 zf-P11: P-11 zinc fin 93.7 0.019 4.1E-07 40.9 0.0 33 299-331 15-48 (50)
96 KOG3268 Predicted E3 ubiquitin 93.3 0.053 1.1E-06 49.1 2.2 50 282-331 166-230 (234)
97 KOG1001 Helicase-like transcri 93.2 0.021 4.5E-07 61.9 -0.6 48 282-333 455-504 (674)
98 KOG2932 E3 ubiquitin ligase in 92.8 0.044 9.6E-07 53.5 1.0 43 282-328 91-133 (389)
99 KOG0298 DEAD box-containing he 92.1 0.064 1.4E-06 60.8 1.3 45 281-327 1153-1197(1394)
100 PF07800 DUF1644: Protein of u 92.1 0.18 3.9E-06 44.9 3.8 53 281-336 2-98 (162)
101 TIGR00100 hypA hydrogenase nic 91.9 0.12 2.6E-06 43.7 2.5 35 20-58 67-101 (115)
102 PRK12380 hydrogenase nickel in 91.1 0.16 3.4E-06 42.9 2.3 35 20-58 67-101 (113)
103 PRK00762 hypA hydrogenase nick 90.9 0.17 3.6E-06 43.4 2.4 38 20-58 67-107 (124)
104 PF01155 HypA: Hydrogenase exp 90.9 0.076 1.7E-06 44.7 0.3 35 20-58 67-101 (113)
105 KOG1100 Predicted E3 ubiquitin 90.7 0.11 2.3E-06 48.5 1.1 40 284-330 161-201 (207)
106 KOG2114 Vacuolar assembly/sort 90.6 0.13 2.9E-06 56.1 1.8 46 280-330 839-884 (933)
107 KOG2817 Predicted E3 ubiquitin 90.5 0.22 4.7E-06 50.2 3.1 49 280-328 333-384 (394)
108 KOG0309 Conserved WD40 repeat- 90.5 0.15 3.2E-06 55.1 2.0 28 296-323 1042-1069(1081)
109 KOG1832 HIV-1 Vpr-binding prot 90.4 0.22 4.7E-06 54.9 3.2 11 117-127 1400-1410(1516)
110 PF14446 Prok-RING_1: Prokaryo 90.4 0.26 5.7E-06 36.2 2.6 33 281-313 5-38 (54)
111 PRK03681 hypA hydrogenase nick 90.3 0.2 4.3E-06 42.3 2.3 36 20-58 67-102 (114)
112 PF09538 FYDLN_acid: Protein o 89.5 0.72 1.6E-05 38.7 5.0 34 21-57 7-40 (108)
113 KOG3002 Zn finger protein [Gen 89.2 0.38 8.1E-06 47.3 3.6 53 280-340 47-101 (299)
114 PRK00564 hypA hydrogenase nick 88.8 0.27 5.8E-06 41.7 2.0 35 20-58 68-103 (117)
115 PF05290 Baculo_IE-1: Baculovi 88.7 0.32 7E-06 42.1 2.4 56 278-333 77-136 (140)
116 COG1996 RPC10 DNA-directed RNA 88.6 0.25 5.4E-06 35.6 1.4 31 22-54 5-35 (49)
117 KOG4367 Predicted Zn-finger pr 88.6 0.25 5.4E-06 50.4 1.9 35 280-317 3-37 (699)
118 KOG2034 Vacuolar sorting prote 87.7 0.33 7.1E-06 53.4 2.2 37 279-316 815-851 (911)
119 KOG1812 Predicted E3 ubiquitin 87.4 0.45 9.7E-06 48.4 3.0 39 280-318 145-184 (384)
120 KOG3899 Uncharacterized conser 87.2 0.28 6E-06 47.7 1.3 31 302-332 325-368 (381)
121 PRK03824 hypA hydrogenase nick 86.0 0.44 9.5E-06 41.4 1.7 39 19-57 66-121 (135)
122 PF06524 NOA36: NOA36 protein; 85.0 0.6 1.3E-05 44.8 2.2 7 24-30 172-178 (314)
123 PF06524 NOA36: NOA36 protein; 84.7 0.66 1.4E-05 44.5 2.4 10 25-34 127-136 (314)
124 KOG1609 Protein involved in mR 84.7 0.43 9.3E-06 46.1 1.2 51 281-331 78-136 (323)
125 KOG4362 Transcriptional regula 84.0 0.25 5.3E-06 53.3 -0.9 46 281-329 21-69 (684)
126 KOG3800 Predicted E3 ubiquitin 83.8 0.86 1.9E-05 44.3 2.8 47 283-329 2-51 (300)
127 PF02891 zf-MIZ: MIZ/SP-RING z 83.8 1.3 2.8E-05 31.9 3.0 43 282-327 3-50 (50)
128 smart00834 CxxC_CXXC_SSSS Puta 82.3 1 2.3E-05 30.2 2.0 29 23-51 5-34 (41)
129 KOG3053 Uncharacterized conser 82.0 0.55 1.2E-05 44.9 0.7 49 280-328 19-81 (293)
130 KOG0269 WD40 repeat-containing 81.5 1.3 2.7E-05 48.3 3.2 44 282-326 780-825 (839)
131 COG5183 SSM4 Protein involved 81.3 0.82 1.8E-05 50.0 1.7 52 280-332 11-69 (1175)
132 COG4391 Uncharacterized protei 81.0 1 2.2E-05 33.9 1.6 22 32-54 38-59 (62)
133 PF02724 CDC45: CDC45-like pro 80.4 1 2.3E-05 48.5 2.2 18 236-253 253-270 (622)
134 KOG1829 Uncharacterized conser 80.2 0.62 1.3E-05 49.6 0.4 42 280-324 510-556 (580)
135 KOG4718 Non-SMC (structural ma 79.3 1.2 2.6E-05 41.5 1.9 49 281-331 181-229 (235)
136 PRK07591 threonine synthase; V 79.3 1.5 3.2E-05 45.0 2.8 32 19-56 14-45 (421)
137 KOG1189 Global transcriptional 79.0 2 4.3E-05 46.9 3.7 10 86-95 846-855 (960)
138 COG5220 TFB3 Cdk activating ki 78.4 0.72 1.6E-05 43.8 0.2 47 280-326 9-61 (314)
139 KOG3113 Uncharacterized conser 76.1 4.9 0.00011 38.6 5.0 50 281-332 111-161 (293)
140 TIGR02098 MJ0042_CXXC MJ0042 f 75.9 1.4 3.1E-05 29.4 1.1 32 23-54 2-36 (38)
141 PRK00398 rpoP DNA-directed RNA 75.7 2.7 5.9E-05 29.4 2.5 33 23-57 3-35 (46)
142 COG5270 PUA domain (predicted 75.5 1.5 3.2E-05 40.2 1.3 27 21-55 12-38 (202)
143 PF14803 Nudix_N_2: Nudix N-te 75.4 1.6 3.5E-05 29.0 1.2 26 25-50 2-29 (34)
144 KOG3161 Predicted E3 ubiquitin 74.8 1.3 2.8E-05 47.4 1.0 40 281-322 11-51 (861)
145 KOG0825 PHD Zn-finger protein 74.5 1.7 3.8E-05 47.5 1.8 49 282-330 97-155 (1134)
146 KOG1815 Predicted E3 ubiquitin 74.3 1.5 3.3E-05 45.3 1.3 36 280-317 69-104 (444)
147 KOG0943 Predicted ubiquitin-pr 73.7 2.4 5.2E-05 48.6 2.6 10 177-186 1791-1800(3015)
148 KOG2068 MOT2 transcription fac 73.2 2.5 5.5E-05 41.9 2.5 50 282-331 250-300 (327)
149 PF14353 CpXC: CpXC protein 71.6 2.3 5E-05 36.1 1.6 33 25-57 3-52 (128)
150 PF09723 Zn-ribbon_8: Zinc rib 71.3 4.5 9.8E-05 27.9 2.7 33 23-55 5-38 (42)
151 PF02724 CDC45: CDC45-like pro 71.1 2.2 4.9E-05 46.0 1.7 14 23-36 54-67 (622)
152 KOG1812 Predicted E3 ubiquitin 69.2 2.4 5.2E-05 43.1 1.4 44 280-324 305-351 (384)
153 PF08271 TF_Zn_Ribbon: TFIIB z 68.8 3.3 7.1E-05 28.6 1.6 30 24-56 1-30 (43)
154 TIGR02605 CxxC_CxxC_SSSS putat 68.6 4.9 0.00011 28.5 2.5 35 23-57 5-40 (52)
155 KOG0802 E3 ubiquitin ligase [P 68.6 2.1 4.7E-05 45.3 0.9 46 280-332 478-523 (543)
156 smart00659 RPOLCX RNA polymera 67.8 3.8 8.1E-05 28.8 1.7 29 23-54 2-30 (44)
157 PF13240 zinc_ribbon_2: zinc-r 66.9 2.4 5.2E-05 25.6 0.5 22 25-52 1-22 (23)
158 PF13901 DUF4206: Domain of un 65.8 4 8.8E-05 37.7 2.0 42 280-326 151-197 (202)
159 KOG3576 Ovo and related transc 65.7 1.5 3.3E-05 40.9 -0.8 71 16-93 110-192 (267)
160 KOG3579 Predicted E3 ubiquitin 65.5 3.9 8.4E-05 39.9 1.9 38 281-319 268-307 (352)
161 PRK06266 transcription initiat 63.5 2.8 6.1E-05 38.1 0.5 36 20-56 114-149 (178)
162 KOG2807 RNA polymerase II tran 63.5 5.6 0.00012 39.5 2.6 48 280-327 329-376 (378)
163 COG2093 DNA-directed RNA polym 63.4 3.1 6.8E-05 31.4 0.7 29 25-59 6-35 (64)
164 PF10276 zf-CHCC: Zinc-finger 63.4 4 8.7E-05 28.2 1.1 22 33-54 19-40 (40)
165 PRK14892 putative transcriptio 63.4 7.1 0.00015 32.3 2.8 38 21-58 19-57 (99)
166 PF05191 ADK_lid: Adenylate ki 63.2 2.6 5.6E-05 28.3 0.2 33 23-55 1-33 (36)
167 smart00661 RPOL9 RNA polymeras 62.5 4.9 0.00011 28.3 1.6 32 25-58 2-33 (52)
168 COG1439 Predicted nucleic acid 62.0 4.5 9.8E-05 36.8 1.6 27 21-53 137-163 (177)
169 PF14968 CCDC84: Coiled coil p 61.8 4.2 9.1E-05 40.7 1.4 34 19-60 54-87 (336)
170 TIGR00373 conserved hypothetic 61.7 2.7 5.8E-05 37.4 0.1 35 20-55 106-140 (158)
171 smart00132 LIM Zinc-binding do 61.7 7.2 0.00016 25.0 2.2 38 283-329 1-38 (39)
172 KOG1189 Global transcriptional 61.5 7 0.00015 42.9 3.1 12 175-186 931-942 (960)
173 PF06844 DUF1244: Protein of u 61.3 4.8 0.0001 30.8 1.3 13 305-317 11-23 (68)
174 PF03604 DNA_RNApol_7kD: DNA d 60.8 6.6 0.00014 25.7 1.8 26 24-52 1-26 (32)
175 TIGR02300 FYDLN_acid conserved 59.4 6.3 0.00014 34.0 1.9 34 21-57 7-40 (129)
176 COG5109 Uncharacterized conser 59.1 7.7 0.00017 38.4 2.7 46 280-325 335-383 (396)
177 smart00249 PHD PHD zinc finger 58.3 5.6 0.00012 26.5 1.2 31 283-313 1-31 (47)
178 KOG3507 DNA-directed RNA polym 58.1 10 0.00023 28.3 2.6 38 9-50 4-44 (62)
179 PF13717 zinc_ribbon_4: zinc-r 58.1 5.8 0.00013 26.5 1.2 30 24-53 3-35 (36)
180 KOG3039 Uncharacterized conser 57.8 6.4 0.00014 37.7 1.8 32 282-316 44-75 (303)
181 PF10571 UPF0547: Uncharacteri 57.7 5.2 0.00011 25.0 0.8 23 26-54 3-25 (26)
182 PF13453 zf-TFIIB: Transcripti 57.4 4.8 0.0001 27.4 0.7 30 26-55 2-31 (41)
183 smart00531 TFIIE Transcription 57.2 5.1 0.00011 35.1 1.0 40 19-58 95-138 (147)
184 KOG2066 Vacuolar assembly/sort 56.8 5.5 0.00012 43.8 1.4 46 281-327 784-833 (846)
185 KOG3005 GIY-YIG type nuclease 56.5 5.9 0.00013 38.3 1.4 48 282-329 183-243 (276)
186 PF05605 zf-Di19: Drought indu 55.3 5.4 0.00012 28.8 0.8 10 44-53 3-12 (54)
187 PF05764 YL1: YL1 nuclear prot 55.2 12 0.00027 35.5 3.3 11 85-95 12-22 (240)
188 PF07295 DUF1451: Protein of u 54.9 8.7 0.00019 33.9 2.1 32 19-52 108-139 (146)
189 PF07975 C1_4: TFIIH C1-like d 54.7 8.7 0.00019 27.9 1.7 41 284-324 2-49 (51)
190 PF00628 PHD: PHD-finger; Int 54.5 6.2 0.00013 27.6 0.9 43 283-325 1-49 (51)
191 PF03107 C1_2: C1 domain; Int 54.3 6.1 0.00013 25.2 0.8 22 24-50 1-22 (30)
192 KOG3842 Adaptor protein Pellin 52.9 12 0.00027 37.0 2.9 52 280-331 340-416 (429)
193 cd00350 rubredoxin_like Rubred 52.5 11 0.00024 24.5 1.8 26 23-52 1-26 (33)
194 PF07754 DUF1610: Domain of un 52.2 9 0.0002 23.6 1.2 22 26-51 1-24 (24)
195 PF14787 zf-CCHC_5: GAG-polypr 51.2 6.9 0.00015 26.4 0.7 11 44-54 3-13 (36)
196 COG5406 Nucleosome binding fac 50.7 15 0.00032 39.8 3.3 9 87-95 899-907 (1001)
197 PF00096 zf-C2H2: Zinc finger, 50.7 5.2 0.00011 23.2 -0.0 12 44-55 1-12 (23)
198 PF10263 SprT-like: SprT-like 49.9 9.8 0.00021 32.9 1.7 35 21-55 121-155 (157)
199 PF06827 zf-FPG_IleRS: Zinc fi 49.4 8.2 0.00018 24.4 0.8 27 25-51 3-29 (30)
200 smart00647 IBR In Between Ring 48.5 14 0.0003 26.7 2.1 42 21-62 16-59 (64)
201 PF01363 FYVE: FYVE zinc finge 48.4 9.8 0.00021 28.5 1.2 37 279-315 7-44 (69)
202 KOG4185 Predicted E3 ubiquitin 48.2 3.6 7.9E-05 39.7 -1.5 47 281-327 207-265 (296)
203 KOG0824 Predicted E3 ubiquitin 47.9 6.5 0.00014 38.7 0.2 47 280-329 104-151 (324)
204 KOG0699 Serine/threonine prote 47.8 14 0.0003 37.5 2.4 19 259-277 413-431 (542)
205 PF03344 Daxx: Daxx Family; I 47.4 6.2 0.00014 43.3 0.0 9 321-329 651-659 (713)
206 TIGR00622 ssl1 transcription f 47.0 18 0.00038 30.6 2.6 44 282-325 56-110 (112)
207 TIGR03831 YgiT_finger YgiT-typ 46.9 9.8 0.00021 25.8 0.9 20 36-55 25-44 (46)
208 PF13719 zinc_ribbon_5: zinc-r 46.7 12 0.00027 25.0 1.4 30 25-54 4-36 (37)
209 PRK12496 hypothetical protein; 46.7 11 0.00023 33.9 1.4 27 23-53 127-153 (164)
210 PF04710 Pellino: Pellino; In 46.5 6.6 0.00014 40.0 0.0 32 296-330 303-340 (416)
211 KOG2169 Zn-finger transcriptio 46.4 20 0.00043 39.0 3.6 55 280-338 305-365 (636)
212 PF14812 PBP1_TM: Transmembran 45.4 7 0.00015 31.2 0.0 6 209-214 67-72 (81)
213 PF13465 zf-H2C2_2: Zinc-finge 45.2 7.2 0.00016 23.9 0.0 11 44-54 15-25 (26)
214 TIGR01206 lysW lysine biosynth 45.2 12 0.00026 27.5 1.2 32 23-54 2-33 (54)
215 PF04710 Pellino: Pellino; In 44.2 7.5 0.00016 39.6 0.0 50 281-330 328-402 (416)
216 KOG1597 Transcription initiati 43.1 14 0.0003 36.3 1.6 29 25-53 2-31 (308)
217 PRK05452 anaerobic nitric oxid 43.0 20 0.00043 37.5 2.9 36 13-52 415-467 (479)
218 KOG2038 CAATT-binding transcri 42.9 15 0.00033 40.5 2.1 6 241-246 971-976 (988)
219 PF14569 zf-UDP: Zinc-binding 42.7 26 0.00056 27.8 2.8 49 280-328 8-61 (80)
220 PHA00616 hypothetical protein 42.0 6.4 0.00014 27.8 -0.6 13 44-56 2-14 (44)
221 COG1198 PriA Primosomal protei 40.6 16 0.00034 40.4 1.7 31 20-57 459-489 (730)
222 KOG4317 Predicted Zn-finger pr 40.4 15 0.00032 36.5 1.3 26 21-54 5-30 (383)
223 PF09788 Tmemb_55A: Transmembr 40.1 24 0.00053 33.9 2.7 32 20-51 154-185 (256)
224 PF10497 zf-4CXXC_R1: Zinc-fin 39.9 24 0.00052 29.3 2.4 24 303-326 37-69 (105)
225 TIGR00155 pqiA_fam integral me 39.8 17 0.00036 37.3 1.7 29 25-53 15-43 (403)
226 PF04216 FdhE: Protein involve 39.1 3.5 7.5E-05 40.1 -3.2 48 280-327 171-220 (290)
227 KOG3993 Transcription factor ( 38.8 15 0.00032 37.9 1.1 29 27-62 286-314 (500)
228 PF06937 EURL: EURL protein; 38.7 36 0.00079 33.0 3.7 56 281-340 30-88 (285)
229 PF01485 IBR: IBR domain; Int 38.6 11 0.00025 27.1 0.2 30 24-53 19-50 (64)
230 COG3043 NapB Nitrate reductase 37.8 18 0.00038 32.1 1.3 19 16-36 119-137 (155)
231 PRK15103 paraquat-inducible me 37.7 18 0.00039 37.3 1.6 30 24-53 11-40 (419)
232 PF13894 zf-C2H2_4: C2H2-type 37.7 14 0.0003 20.9 0.5 11 44-54 1-11 (24)
233 KOG1729 FYVE finger containing 37.4 7.6 0.00017 38.1 -1.1 40 280-319 213-252 (288)
234 PF05285 SDA1: SDA1; InterPro 37.3 19 0.00041 35.8 1.6 11 84-94 67-77 (324)
235 PRK13794 hypothetical protein; 37.1 16 0.00035 38.2 1.2 23 22-52 9-31 (479)
236 KOG1991 Nuclear transport rece 36.9 19 0.0004 40.7 1.6 7 241-247 978-984 (1010)
237 PTZ00415 transmission-blocking 36.3 22 0.00048 42.6 2.1 22 37-58 87-108 (2849)
238 PLN02638 cellulose synthase A 35.8 32 0.00069 39.5 3.2 49 281-329 17-70 (1079)
239 cd00065 FYVE FYVE domain; Zinc 35.4 24 0.00051 25.2 1.5 35 282-316 3-38 (57)
240 KOG1074 Transcriptional repres 35.4 12 0.00025 41.6 -0.2 54 9-62 862-926 (958)
241 COG3492 Uncharacterized protei 35.1 19 0.00041 29.4 1.0 13 305-317 42-54 (104)
242 smart00154 ZnF_AN1 AN1-like Zi 34.9 20 0.00043 24.4 1.0 24 26-55 1-24 (39)
243 PF00412 LIM: LIM domain; Int 34.5 25 0.00055 24.8 1.5 40 284-332 1-40 (58)
244 smart00109 C1 Protein kinase C 34.3 19 0.00042 24.3 0.9 24 23-50 11-34 (49)
245 KOG2113 Predicted RNA binding 34.3 37 0.00079 33.8 3.0 46 280-330 342-388 (394)
246 PF04423 Rad50_zn_hook: Rad50 34.3 12 0.00025 27.0 -0.3 13 320-332 22-34 (54)
247 PF06750 DiS_P_DiS: Bacterial 34.1 34 0.00073 27.7 2.3 44 281-336 33-76 (92)
248 PF05285 SDA1: SDA1; InterPro 33.9 20 0.00043 35.6 1.1 7 85-91 28-34 (324)
249 KOG1074 Transcriptional repres 33.8 12 0.00027 41.4 -0.4 70 278-347 602-697 (958)
250 PLN02436 cellulose synthase A 33.7 37 0.00079 39.0 3.3 49 281-329 36-89 (1094)
251 KOG2141 Protein involved in hi 33.6 24 0.00052 38.7 1.7 12 324-335 471-482 (822)
252 COG4338 Uncharacterized protei 33.6 14 0.0003 26.6 -0.0 15 39-53 8-22 (54)
253 KOG4443 Putative transcription 33.3 17 0.00038 39.2 0.7 27 301-327 40-71 (694)
254 PLN02189 cellulose synthase 33.2 39 0.00084 38.7 3.3 49 281-329 34-87 (1040)
255 PF13832 zf-HC5HC2H_2: PHD-zin 33.2 34 0.00073 27.9 2.3 33 280-314 54-88 (110)
256 KOG2141 Protein involved in hi 33.0 20 0.00043 39.3 1.1 13 50-62 102-114 (822)
257 PF06906 DUF1272: Protein of u 33.0 62 0.0013 24.1 3.3 45 283-329 7-52 (57)
258 PHA00626 hypothetical protein 32.9 32 0.00069 25.6 1.8 31 25-55 2-35 (59)
259 PF13824 zf-Mss51: Zinc-finger 32.0 24 0.00051 26.1 1.0 21 25-50 1-21 (55)
260 PRK01343 zinc-binding protein; 31.7 26 0.00057 26.1 1.2 18 37-54 3-20 (57)
261 PF06220 zf-U1: U1 zinc finger 31.5 16 0.00034 24.8 -0.0 12 22-33 2-13 (38)
262 TIGR00595 priA primosomal prot 31.5 29 0.00063 36.5 2.0 29 21-56 238-266 (505)
263 PF07282 OrfB_Zn_ribbon: Putat 31.4 26 0.00057 26.1 1.2 24 26-51 31-54 (69)
264 PRK14873 primosome assembly pr 31.2 28 0.0006 38.1 1.8 29 21-57 408-436 (665)
265 PF12773 DZR: Double zinc ribb 31.2 22 0.00048 24.8 0.7 28 21-51 10-37 (50)
266 PF02318 FYVE_2: FYVE-type zin 31.1 27 0.00059 29.3 1.4 46 280-326 53-102 (118)
267 PF13248 zf-ribbon_3: zinc-rib 30.6 22 0.00047 21.9 0.5 23 24-52 3-25 (26)
268 TIGR01405 polC_Gram_pos DNA po 29.6 26 0.00056 41.0 1.3 34 21-54 681-719 (1213)
269 PRK11032 hypothetical protein; 29.6 39 0.00084 30.3 2.2 32 20-53 121-152 (160)
270 PF07649 C1_3: C1-like domain; 29.5 34 0.00074 21.5 1.3 29 283-311 2-30 (30)
271 KOG1245 Chromatin remodeling c 29.4 18 0.0004 42.7 0.1 49 280-328 1107-1159(1404)
272 TIGR03830 CxxCG_CxxCG_HTH puta 29.4 31 0.00067 28.6 1.5 15 40-54 28-42 (127)
273 PF07191 zinc-ribbons_6: zinc- 29.3 29 0.00063 26.9 1.1 24 21-51 15-38 (70)
274 PF00130 C1_1: Phorbol esters/ 29.2 31 0.00067 24.3 1.2 27 22-51 10-36 (53)
275 KOG2462 C2H2-type Zn-finger pr 29.1 36 0.00079 33.1 2.0 38 18-55 125-173 (279)
276 COG4847 Uncharacterized protei 29.0 56 0.0012 26.9 2.7 36 281-317 6-41 (103)
277 PLN02400 cellulose synthase 29.0 40 0.00086 38.8 2.6 49 281-329 36-89 (1085)
278 KOG2897 DNA-binding protein YL 28.8 44 0.00096 33.9 2.6 14 320-333 295-308 (390)
279 PLN02195 cellulose synthase A 28.8 62 0.0013 36.9 4.0 49 281-329 6-59 (977)
280 KOG4451 Uncharacterized conser 28.4 37 0.0008 32.3 1.8 31 304-334 249-279 (286)
281 PHA00733 hypothetical protein 27.9 24 0.00053 30.2 0.6 36 21-56 71-112 (128)
282 KOG2231 Predicted E3 ubiquitin 27.4 37 0.0008 37.1 1.9 45 283-330 2-53 (669)
283 PRK10220 hypothetical protein; 27.2 36 0.00079 28.6 1.4 27 26-56 6-33 (111)
284 PF01783 Ribosomal_L32p: Ribos 27.2 24 0.00052 25.9 0.3 23 23-54 26-48 (56)
285 COG2995 PqiA Uncharacterized p 26.8 30 0.00065 35.4 1.1 32 20-51 15-46 (418)
286 KOG1824 TATA-binding protein-i 26.4 29 0.00064 39.3 1.0 9 244-252 435-443 (1233)
287 PRK11088 rrmA 23S rRNA methylt 26.3 41 0.00089 32.0 1.8 26 282-307 3-28 (272)
288 smart00064 FYVE Protein presen 26.2 48 0.001 24.6 1.8 36 281-316 10-46 (68)
289 TIGR00686 phnA alkylphosphonat 26.1 35 0.00077 28.7 1.2 28 26-56 5-32 (109)
290 PF10146 zf-C4H2: Zinc finger- 25.9 47 0.001 31.5 2.1 29 306-334 196-224 (230)
291 PF09943 DUF2175: Uncharacteri 25.9 55 0.0012 27.2 2.2 34 282-316 3-36 (101)
292 PF10013 DUF2256: Uncharacteri 25.6 39 0.00086 23.6 1.1 16 39-54 4-19 (42)
293 PF11682 DUF3279: Protein of u 25.3 32 0.0007 29.7 0.8 18 13-30 18-35 (128)
294 KOG1842 FYVE finger-containing 24.8 57 0.0012 33.9 2.6 42 272-314 171-214 (505)
295 PF03811 Zn_Tnp_IS1: InsA N-te 24.6 37 0.00081 22.8 0.9 10 43-52 5-14 (36)
296 KOG0127 Nucleolar protein fibr 24.1 49 0.0011 35.3 2.0 12 51-62 141-152 (678)
297 COG3813 Uncharacterized protei 24.1 50 0.0011 25.9 1.6 47 284-332 8-55 (84)
298 PF12674 Zn_ribbon_2: Putative 24.1 27 0.00059 27.7 0.1 32 25-56 2-41 (81)
299 PF10122 Mu-like_Com: Mu-like 24.0 25 0.00053 25.6 -0.1 31 23-53 4-34 (51)
300 PF09845 DUF2072: Zn-ribbon co 23.8 60 0.0013 28.2 2.2 40 23-64 1-40 (131)
301 COG5137 Histone chaperone invo 23.8 47 0.001 31.4 1.6 12 44-55 97-108 (279)
302 KOG2113 Predicted RNA binding 23.7 26 0.00057 34.8 -0.0 45 281-328 136-182 (394)
303 COG1645 Uncharacterized Zn-fin 23.7 48 0.001 28.8 1.6 28 23-54 28-55 (131)
304 PF09779 Ima1_N: Ima1 N-termin 23.5 52 0.0011 28.3 1.8 25 26-50 3-27 (131)
305 PRK00432 30S ribosomal protein 23.4 34 0.00073 24.6 0.5 11 45-55 22-32 (50)
306 KOG1815 Predicted E3 ubiquitin 23.4 24 0.00053 36.5 -0.3 36 283-318 228-268 (444)
307 PF14283 DUF4366: Domain of un 22.9 57 0.0012 30.7 2.0 11 113-123 178-188 (218)
308 cd00029 C1 Protein kinase C co 22.9 37 0.0008 23.2 0.6 25 23-50 11-35 (50)
309 PF05280 FlhC: Flagellar trans 22.8 35 0.00077 31.0 0.7 27 24-50 135-161 (175)
310 PRK06260 threonine synthase; V 22.5 47 0.001 33.6 1.6 25 23-51 3-27 (397)
311 TIGR01562 FdhE formate dehydro 22.4 20 0.00043 35.5 -1.1 45 281-326 184-232 (305)
312 KOG0883 Cyclophilin type, U bo 22.3 64 0.0014 33.1 2.3 50 282-334 41-90 (518)
313 PRK13795 hypothetical protein; 22.3 55 0.0012 35.6 2.1 29 21-58 10-38 (636)
314 KOG3726 Uncharacterized conser 22.2 45 0.00098 36.4 1.4 41 282-325 655-696 (717)
315 cd00730 rubredoxin Rubredoxin; 22.2 62 0.0013 23.3 1.7 10 43-52 34-43 (50)
316 PRK05580 primosome assembly pr 22.2 54 0.0012 35.9 2.0 29 21-56 406-434 (679)
317 KOG3799 Rab3 effector RIM1 and 21.9 20 0.00044 31.3 -1.0 58 280-337 64-128 (169)
318 TIGR01384 TFS_arch transcripti 21.8 49 0.0011 26.9 1.2 24 25-52 2-25 (104)
319 KOG1834 Calsyntenin [Extracell 21.6 50 0.0011 36.0 1.6 8 52-59 772-779 (952)
320 COG1579 Zn-ribbon protein, pos 21.4 34 0.00073 32.7 0.2 32 20-51 194-229 (239)
321 KOG4218 Nuclear hormone recept 21.4 68 0.0015 32.4 2.3 64 279-343 13-93 (475)
322 PLN02248 cellulose synthase-li 21.3 75 0.0016 36.8 2.9 36 297-332 145-180 (1135)
323 PF13913 zf-C2HC_2: zinc-finge 21.3 35 0.00075 20.8 0.2 12 44-55 3-14 (25)
324 PRK14890 putative Zn-ribbon RN 21.3 57 0.0012 24.5 1.4 30 21-50 23-55 (59)
325 COG2331 Uncharacterized protei 21.3 25 0.00054 27.8 -0.6 38 20-57 9-47 (82)
326 PHA02768 hypothetical protein; 21.1 27 0.00059 25.8 -0.3 33 22-54 4-42 (55)
327 PF04438 zf-HIT: HIT zinc fing 21.0 54 0.0012 21.0 1.1 21 23-52 2-22 (30)
328 PF12156 ATPase-cat_bd: Putati 21.0 38 0.00083 27.1 0.4 27 26-52 3-35 (88)
329 KOG3064 RNA-binding nuclear pr 20.9 47 0.001 32.2 1.1 53 125-177 209-261 (303)
330 KOG3183 Predicted Zn-finger pr 20.9 40 0.00087 32.2 0.6 31 301-331 28-68 (250)
331 PRK05654 acetyl-CoA carboxylas 20.9 31 0.00066 33.9 -0.2 31 22-53 26-56 (292)
332 PRK05978 hypothetical protein; 20.8 50 0.0011 29.3 1.2 20 313-332 47-66 (148)
333 COG3357 Predicted transcriptio 20.7 48 0.001 27.1 0.9 30 25-56 60-89 (97)
334 smart00731 SprT SprT homologue 20.4 80 0.0017 27.3 2.4 35 21-55 110-145 (146)
335 PF12760 Zn_Tnp_IS1595: Transp 20.3 43 0.00093 23.3 0.5 9 44-52 19-27 (46)
336 COG1675 TFA1 Transcription ini 20.3 30 0.00066 31.5 -0.3 36 19-55 109-144 (176)
337 PF14255 Cys_rich_CPXG: Cystei 20.2 42 0.0009 24.5 0.4 14 44-57 1-14 (52)
338 KOG2071 mRNA cleavage and poly 20.2 52 0.0011 35.3 1.3 37 279-315 511-557 (579)
339 PF08772 NOB1_Zn_bind: Nin one 20.1 56 0.0012 25.5 1.2 32 24-60 10-41 (73)
No 1
>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=99.50 E-value=6.6e-15 Score=103.29 Aligned_cols=43 Identities=53% Similarity=1.265 Sum_probs=40.3
Q ss_pred cccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR 325 (363)
.|+||++.|..++.++.++|+|+||..||.+|++.+++||+||
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 6999999999888999999999999999999999999999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.49 E-value=2e-14 Score=141.01 Aligned_cols=77 Identities=32% Similarity=0.709 Sum_probs=67.0
Q ss_pred CCChhhHHHHHcCCceeeecccccc---cccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCCh
Q 017955 258 GAPRAAKSAVLELPTVEILSEQETI---VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDDP 333 (363)
Q Consensus 258 ~~~~~s~~~i~~lp~~~~~~~~~~~---~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d~ 333 (363)
......+..++.+|...++...... .|+|||+.|..|+.+++|||+|.||..||.+||.++. .||+|++.+.+...
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG 282 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence 5567789999999999988766544 8999999999999999999999999999999998775 59999999976654
Q ss_pred h
Q 017955 334 E 334 (363)
Q Consensus 334 ~ 334 (363)
.
T Consensus 283 ~ 283 (348)
T KOG4628|consen 283 S 283 (348)
T ss_pred C
Confidence 4
No 3
>PF14369 zf-RING_3: zinc-finger
Probab=99.41 E-value=7.7e-14 Score=93.44 Aligned_cols=34 Identities=47% Similarity=1.079 Sum_probs=28.2
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
+||||+|+++|++... ..++++||+|++||||||
T Consensus 2 ~ywCh~C~~~V~~~~~-~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS-PDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CEeCccCCCEeEeCcC-CCCCcCCcCCCCcEeEeC
Confidence 7999999988887655 333456999999999997
No 4
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.23 E-value=1.2e-11 Score=116.38 Aligned_cols=68 Identities=32% Similarity=0.576 Sum_probs=53.1
Q ss_pred hhHHHHHcCCceeeec-----ccccccccccccccccCC-----ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 262 AAKSAVLELPTVEILS-----EQETIVCAICKDTVNVGE-----TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 262 ~s~~~i~~lp~~~~~~-----~~~~~~C~ICle~f~~~e-----~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
..+..+..+|.+.... ...+..|+||++.+.... .+..++|+|.||..||.+|++.+.+||+||..+.
T Consensus 150 ~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 150 NYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred hhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 3678888888776432 224678999999876433 1344569999999999999999999999999875
No 5
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.21 E-value=8.7e-12 Score=97.10 Aligned_cols=46 Identities=41% Similarity=0.972 Sum_probs=36.7
Q ss_pred cccccccccccccc----------CCceEEeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955 280 ETIVCAICKDTVNV----------GETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325 (363)
Q Consensus 280 ~~~~C~ICle~f~~----------~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR 325 (363)
.+..|+||++.|.. .-.+...+|+|.||..||.+||+.+++||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 34569999999932 12455567999999999999999999999998
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.18 E-value=1.3e-11 Score=120.43 Aligned_cols=68 Identities=34% Similarity=0.731 Sum_probs=51.0
Q ss_pred hhHHHHHcCCceeeec-ccccccccccccc-cccC---------CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 262 AAKSAVLELPTVEILS-EQETIVCAICKDT-VNVG---------ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 262 ~s~~~i~~lp~~~~~~-~~~~~~C~ICle~-f~~~---------e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
+.|..-+.++++...+ ...+..|.||++. |..+ -.+++|||||+||..|++.|+++.++||+||.++-
T Consensus 267 ~~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 267 ATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred HhhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 3344444444444333 3367889999998 4433 25799999999999999999999999999999954
No 7
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.14 E-value=2.3e-11 Score=116.10 Aligned_cols=51 Identities=37% Similarity=0.881 Sum_probs=46.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~~ 330 (363)
..-.|+|||+.|..++..+.|||+|.||..||.+|+. -++.||+||.++|+
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 4467999999999888999999999999999999998 57799999999986
No 8
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=5e-11 Score=113.38 Aligned_cols=51 Identities=27% Similarity=0.843 Sum_probs=46.0
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~ 333 (363)
...+|.|||+... .+..+||||+||..||..|+..+..||+||..+++...
T Consensus 238 a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence 4578999999876 78899999999999999999999999999999987654
No 9
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=99.02 E-value=1.8e-10 Score=82.88 Aligned_cols=46 Identities=30% Similarity=0.833 Sum_probs=40.1
Q ss_pred cccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
+..|.||++.+. .+..+||+|. ||..|+..|++.+..||+||++|.
T Consensus 2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 467999999876 6888999999 999999999999999999999875
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.01 E-value=2.4e-10 Score=103.94 Aligned_cols=55 Identities=27% Similarity=0.597 Sum_probs=44.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc----------------CCCCCCcCcCCCCCChhHHH
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS----------------RNTCPVCRFELPTDDPEYEE 337 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~----------------~~sCPlCR~~l~~~d~~~~~ 337 (363)
....|+||++.+. .++.++|+|.||..||.+|+.. ...||+||..|...+...-.
T Consensus 17 ~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 17 GDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred CccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence 5678999999987 5677899999999999999853 24799999999876644433
No 11
>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=98.96 E-value=4.2e-10 Score=76.90 Aligned_cols=39 Identities=38% Similarity=1.022 Sum_probs=33.4
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCc
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlC 324 (363)
|+||++.+.. .++.++|||.||..||.+|++.+..||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999999883 44788999999999999999998899998
No 12
>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=98.95 E-value=6.8e-10 Score=76.08 Aligned_cols=44 Identities=48% Similarity=1.131 Sum_probs=36.6
Q ss_pred cccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCC
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFEL 328 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l 328 (363)
.|+||++.+. .....++|+|.||..||..|++. +..||+||..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4999999983 34555559999999999999998 67899999864
No 13
>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=98.91 E-value=1.2e-09 Score=81.59 Aligned_cols=52 Identities=29% Similarity=0.484 Sum_probs=44.9
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHH
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYE 336 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~ 336 (363)
..|+||++.+. .++.++|||+|++.||.+|++.+.+||+|+..+...+....
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~ 53 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN 53 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence 46999999988 46788999999999999999998999999999976654443
No 14
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.88 E-value=1.4e-09 Score=75.84 Aligned_cols=38 Identities=34% Similarity=0.955 Sum_probs=31.0
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCc
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlC 324 (363)
|+||++.|. .++.|+|||.||..||..|++... .||+|
T Consensus 1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999998 789999999999999999997643 69988
No 15
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=7.7e-10 Score=102.55 Aligned_cols=50 Identities=34% Similarity=0.848 Sum_probs=42.3
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC---CCCCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR---NTCPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~---~sCPlCR~~l~~~d 332 (363)
....|.|||+.-+ .++...|||.||+.||.+||+.+ +.||+|+..|..+.
T Consensus 46 ~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 46 GFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 4567999999876 67778899999999999999864 47999999887665
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=1.3e-09 Score=97.20 Aligned_cols=51 Identities=35% Similarity=0.771 Sum_probs=42.9
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
....|+|||+.+... .+.-..|||+||..||+.-++....||+||+.|..+
T Consensus 130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 447799999998842 334567999999999999999999999999987654
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=98.81 E-value=2.2e-09 Score=99.10 Aligned_cols=52 Identities=29% Similarity=0.698 Sum_probs=39.2
Q ss_pred ccccccccccccccC-----CceEEe-CCCCcccHhhHHHHHhcC------CCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVG-----ETATKL-PCGHVYHGDCIVPWLDSR------NTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~-----e~~~~L-PC~H~Fh~~CI~~WLk~~------~sCPlCR~~l~~~ 331 (363)
.+..|+|||+..... .....| +|+|.||..||..|.+.+ .+||+||..+..-
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 568899999976422 122344 599999999999999753 3699999987643
No 18
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.79 E-value=1.7e-09 Score=113.44 Aligned_cols=49 Identities=37% Similarity=1.090 Sum_probs=43.6
Q ss_pred ccccccccccccccCCc--eEEeCCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGET--ATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~--~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l 328 (363)
....|+||++.+..+.. +++|||+|+||..||+.|+++.++||+||..+
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 46789999999985543 89999999999999999999999999999933
No 19
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.79 E-value=3.7e-09 Score=84.17 Aligned_cols=51 Identities=31% Similarity=0.787 Sum_probs=39.2
Q ss_pred cccccccccccccc--------CC--ceEEeCCCCcccHhhHHHHHhc---CCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNV--------GE--TATKLPCGHVYHGDCIVPWLDS---RNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~--------~e--~~~~LPC~H~Fh~~CI~~WLk~---~~sCPlCR~~l~~ 330 (363)
.+..|.||+..|.. ++ .++.-.|+|.||..||.+||.+ +..||+||+.+..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 47889999998873 11 1222349999999999999986 4589999998754
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.75 E-value=6.5e-09 Score=72.95 Aligned_cols=44 Identities=25% Similarity=0.693 Sum_probs=38.7
Q ss_pred cccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~ 326 (363)
.|+||++.|.....+..++|+|+||..||..+......||+||+
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 49999999965567889999999999999999866779999985
No 21
>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=98.74 E-value=6.5e-09 Score=71.36 Aligned_cols=39 Identities=38% Similarity=1.100 Sum_probs=33.2
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHh--cCCCCCCc
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLD--SRNTCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk--~~~sCPlC 324 (363)
|+||++.+.. ....++|+|.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999999883 334889999999999999999 45589998
No 22
>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=98.72 E-value=1.1e-08 Score=67.66 Aligned_cols=38 Identities=45% Similarity=1.229 Sum_probs=33.3
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCc
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlC 324 (363)
|+||++... .+..++|+|.||..||..|++ .+..||+|
T Consensus 1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 889999844 778899999999999999998 56679987
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.65 E-value=1.6e-08 Score=101.70 Aligned_cols=50 Identities=30% Similarity=0.700 Sum_probs=44.0
Q ss_pred cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
.....|+||++.|. .++.++|+|.||..||..|+.....||+||..+...
T Consensus 24 e~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 35678999999987 556789999999999999999988999999988764
No 24
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.63 E-value=1.7e-08 Score=78.78 Aligned_cols=51 Identities=33% Similarity=0.760 Sum_probs=38.7
Q ss_pred ccccccccccccc------------CCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 281 TIVCAICKDTVNV------------GETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 281 ~~~C~ICle~f~~------------~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
...|.||...|.. ++.+...- |+|.||..||.+||..++.||+||+.+...
T Consensus 20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~ 83 (88)
T COG5194 20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA 83 (88)
T ss_pred cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence 4678888776642 22233333 999999999999999999999999987543
No 25
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=4.2e-08 Score=92.63 Aligned_cols=50 Identities=24% Similarity=0.772 Sum_probs=43.6
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHH-HHhcCCC-CCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVP-WLDSRNT-CPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~-WLk~~~s-CPlCR~~l~~~d 332 (363)
.+..|+||++... .+..+||||+||..||.. |-+++.- ||+||..+..+.
T Consensus 214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 4678999999877 788999999999999999 9887775 999999886654
No 26
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.48 E-value=4.5e-08 Score=95.06 Aligned_cols=51 Identities=27% Similarity=0.696 Sum_probs=46.5
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~ 333 (363)
.-+.|.||++.|. .+.++||+|.||.-||..+|..+..||.|+..+...+.
T Consensus 22 ~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 22 DLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence 4478999999998 78899999999999999999999999999999987664
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=98.47 E-value=1e-07 Score=74.11 Aligned_cols=54 Identities=28% Similarity=0.516 Sum_probs=42.3
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCChhHHH
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDPEYEE 337 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~~~~~ 337 (363)
...|+||.+.|. .++++||||.|.+.||..||+. +.+||+|+..+...+.....
T Consensus 4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~ 58 (73)
T PF04564_consen 4 EFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNR 58 (73)
T ss_dssp GGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-H
T ss_pred ccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECH
Confidence 467999999998 7889999999999999999998 78999999999887655533
No 28
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.43 E-value=9e-08 Score=97.49 Aligned_cols=49 Identities=29% Similarity=0.873 Sum_probs=42.0
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-----CCCCCcCcCCCCCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-----NTCPVCRFELPTDD 332 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-----~sCPlCR~~l~~~d 332 (363)
+..|||||+... .+..+.|||+||..||..+|... ..||+||..|..++
T Consensus 186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 678999999876 67777899999999999998764 48999999988755
No 29
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.40 E-value=2e-07 Score=65.37 Aligned_cols=38 Identities=37% Similarity=0.965 Sum_probs=23.1
Q ss_pred cccccccccc-CCceEEeCCCCcccHhhHHHHHhcCC----CCC
Q 017955 284 CAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDSRN----TCP 322 (363)
Q Consensus 284 C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCP 322 (363)
|+||++ |.. ...++.|+|||+||..||.+|++++. .||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 753 44688999999999999999998642 576
No 30
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.28 E-value=1.9e-07 Score=72.35 Aligned_cols=50 Identities=28% Similarity=0.766 Sum_probs=38.3
Q ss_pred ccccccccccccccC---------CceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955 280 ETIVCAICKDTVNVG---------ETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRFELP 329 (363)
Q Consensus 280 ~~~~C~ICle~f~~~---------e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~~l~ 329 (363)
.+..|.||.-.|..- +.+..+- |.|.||..||.+|+... ..||+||+.+.
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 567899999988732 2233333 89999999999999754 37999999764
No 31
>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=98.27 E-value=6.7e-07 Score=64.39 Aligned_cols=42 Identities=29% Similarity=0.877 Sum_probs=33.3
Q ss_pred cccccccccccCCceEEeCCC-----CcccHhhHHHHHhcC--CCCCCcC
Q 017955 283 VCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSR--NTCPVCR 325 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~--~sCPlCR 325 (363)
.|.||++ +...+.+.++||. |++|..||.+|+..+ .+||+|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4899998 3344566788975 899999999999654 4899995
No 32
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.26 E-value=3.4e-07 Score=87.45 Aligned_cols=47 Identities=30% Similarity=0.704 Sum_probs=42.6
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
.-..|.||.+.|. .+..++|+|.||.-||+..|..+.-||+||.+..
T Consensus 24 s~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hHHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 4478999999998 6788899999999999999999999999998764
No 33
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=5.1e-07 Score=91.41 Aligned_cols=50 Identities=36% Similarity=0.980 Sum_probs=39.3
Q ss_pred cccccccccccccCC---c-----------eEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCC
Q 017955 281 TIVCAICKDTVNVGE---T-----------ATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPT 330 (363)
Q Consensus 281 ~~~C~ICle~f~~~e---~-----------~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~ 330 (363)
...|+|||..+..-. . -...||.|+||..|+..|...-+ .||+||.++++
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 457999999775311 1 22348999999999999999555 99999999985
No 34
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.18 E-value=7.5e-07 Score=95.74 Aligned_cols=52 Identities=27% Similarity=0.758 Sum_probs=39.1
Q ss_pred ccccccccccccccccCC---ceEEe-CCCCcccHhhHHHHHhcC--CCCCCcCcCCC
Q 017955 278 EQETIVCAICKDTVNVGE---TATKL-PCGHVYHGDCIVPWLDSR--NTCPVCRFELP 329 (363)
Q Consensus 278 ~~~~~~C~ICle~f~~~e---~~~~L-PC~H~Fh~~CI~~WLk~~--~sCPlCR~~l~ 329 (363)
-.+...|+||+..+..-+ .-++. .|+|.||..||.+|++.+ ++||+||.+++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 346788999998776211 11222 399999999999999874 58999998876
No 35
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=98.12 E-value=1.1e-06 Score=84.36 Aligned_cols=95 Identities=18% Similarity=0.375 Sum_probs=68.3
Q ss_pred cChhhHHHHHHHHHHhcCCCCCCChhhHHHHHcCCceeeecccccccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955 237 MDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD 316 (363)
Q Consensus 237 ~~~~~~e~Ll~~L~~~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk 316 (363)
++...+.+|.+++......+.+.+ ..-..|..-..+.-........|.|||.-|..+...++++|-|+||..|+-.+|.
T Consensus 72 l~d~~~~~i~~~~~~iikq~~g~p-ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~ 150 (368)
T KOG4445|consen 72 LGDPEFREIQRQIQEIIKQNSGMP-IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLT 150 (368)
T ss_pred CCcHHHHHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHH
Confidence 456788888888887776666643 3334444332232223336678999999999998899999999999999988764
Q ss_pred ------------------c-----CCCCCCcCcCCCCCC
Q 017955 317 ------------------S-----RNTCPVCRFELPTDD 332 (363)
Q Consensus 317 ------------------~-----~~sCPlCR~~l~~~d 332 (363)
. ...||+||..|..+.
T Consensus 151 ~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 151 ECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 1 227999999886544
No 36
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.11 E-value=2e-06 Score=83.83 Aligned_cols=52 Identities=23% Similarity=0.499 Sum_probs=37.4
Q ss_pred cccccccccccccCCc--eEEeCCCCcccHhhHHHHH-hcCCCCCCcCcCCCCCC
Q 017955 281 TIVCAICKDTVNVGET--ATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELPTDD 332 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~--~~~LPC~H~Fh~~CI~~WL-k~~~sCPlCR~~l~~~d 332 (363)
+..||||+..-..... ...-+|||.||..||...| .....||+|+..+...+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 4579999995332222 2233799999999999966 44568999998776544
No 37
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=8.1e-07 Score=84.11 Aligned_cols=50 Identities=36% Similarity=0.883 Sum_probs=41.0
Q ss_pred ccccccccccccccCC-------ceEEeCCCCcccHhhHHHHH--hcCCCCCCcCcCCC
Q 017955 280 ETIVCAICKDTVNVGE-------TATKLPCGHVYHGDCIVPWL--DSRNTCPVCRFELP 329 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e-------~~~~LPC~H~Fh~~CI~~WL--k~~~sCPlCR~~l~ 329 (363)
.+..|+||-..+.... ...+|.|+|+||-.||+-|- -++++||.|+..+-
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 5678999988776443 67889999999999999995 45779999987653
No 38
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=2.6e-06 Score=69.82 Aligned_cols=49 Identities=35% Similarity=0.750 Sum_probs=36.9
Q ss_pred ccccccccccccc-------------cCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955 280 ETIVCAICKDTVN-------------VGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~-------------~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l 328 (363)
....|+||...+- .++..+.. -|+|.||..||.+|||+++.||+|.++.
T Consensus 45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 5577999977542 11222222 3999999999999999999999998764
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=1.4e-06 Score=81.07 Aligned_cols=44 Identities=34% Similarity=0.847 Sum_probs=38.7
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~ 326 (363)
....|+||++.|. .++.+||+|.||..||..|+...-.||.||.
T Consensus 12 ~~~~C~iC~~~~~---~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFR---EPVLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhh---cCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 5678999999999 3488999999999999999995568999993
No 40
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.05 E-value=5.8e-07 Score=69.44 Aligned_cols=49 Identities=31% Similarity=0.701 Sum_probs=23.2
Q ss_pred cccccccccccc-cCCc--eEEe--CCCCcccHhhHHHHHhc----C-------CCCCCcCcCCC
Q 017955 281 TIVCAICKDTVN-VGET--ATKL--PCGHVYHGDCIVPWLDS----R-------NTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~-~~e~--~~~L--PC~H~Fh~~CI~~WLk~----~-------~sCPlCR~~l~ 329 (363)
...|.||+..+. .++. +..- .|+++||..||.+||.. + ..||.|+.+|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 357999999866 3332 2222 39999999999999973 1 15999998774
No 41
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.03 E-value=9.7e-07 Score=93.39 Aligned_cols=51 Identities=24% Similarity=0.459 Sum_probs=46.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
....|+||+..|..+......+|+|+||..||..|.+..++||+||..|-.
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 456899999999988888888999999999999999999999999998753
No 42
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.94 E-value=3.2e-06 Score=81.29 Aligned_cols=49 Identities=33% Similarity=0.573 Sum_probs=42.0
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD 332 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d 332 (363)
...|+||+.... .++.|+|+|.||.-||+--.++.+ +|++||.+|...-
T Consensus 7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 356999999876 678999999999999999887755 6999999997654
No 43
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=6.9e-06 Score=81.43 Aligned_cols=54 Identities=30% Similarity=0.701 Sum_probs=40.2
Q ss_pred cccccccccccccccCC----ceEEeC-CCCcccHhhHHHHH--hc-----CCCCCCcCcCCCCCC
Q 017955 279 QETIVCAICKDTVNVGE----TATKLP-CGHVYHGDCIVPWL--DS-----RNTCPVCRFELPTDD 332 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e----~~~~LP-C~H~Fh~~CI~~WL--k~-----~~sCPlCR~~l~~~d 332 (363)
..+..|.||++...... ...+|| |.|.||..||..|- ++ .+.||.||.......
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~ 224 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN 224 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence 35678999999876322 123445 99999999999997 44 568999998765443
No 44
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=2.7e-06 Score=83.32 Aligned_cols=49 Identities=37% Similarity=0.684 Sum_probs=38.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~ 330 (363)
.+..|+|||..++. ..+..-|.|.||..||.+-|+. ++.||.||+.+-.
T Consensus 42 ~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 42 IQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 45779999998872 3333349999999999998876 5699999997753
No 45
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=1.3e-05 Score=78.83 Aligned_cols=48 Identities=27% Similarity=0.636 Sum_probs=41.6
Q ss_pred ccccccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
....|.|||...+ ...+|||.| -.|..|.+.---+++.||+||++|..
T Consensus 289 ~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 289 SGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred CCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 3578999999877 678999999 68999998877789999999998854
No 46
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.78 E-value=2.2e-05 Score=72.78 Aligned_cols=73 Identities=23% Similarity=0.491 Sum_probs=60.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc--------CCCCCCcCcCCCCC----ChhHHHHHHhhhccCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS--------RNTCPVCRFELPTD----DPEYEEERKKRVSAGA 347 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~--------~~sCPlCR~~l~~~----d~~~~~~~~~~~~~~~ 347 (363)
....|..|--.+..++.+ +|.|-|+||..|+.+|-.+ ...||.|..+|.+. .+..+..|.+...+.|
T Consensus 49 Y~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qvNW 127 (299)
T KOG3970|consen 49 YNPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQVNW 127 (299)
T ss_pred CCCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhhhH
Confidence 345699999988877655 6889999999999999764 22799999988654 4788999999999999
Q ss_pred CCCCCC
Q 017955 348 SVGGAS 353 (363)
Q Consensus 348 ~~~g~~ 353 (363)
+|+|+|
T Consensus 128 aRagLG 133 (299)
T KOG3970|consen 128 ARAGLG 133 (299)
T ss_pred HhhccC
Confidence 999886
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.65 E-value=9.5e-06 Score=61.30 Aligned_cols=49 Identities=27% Similarity=0.604 Sum_probs=24.2
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~ 333 (363)
-..|+||.+.++. .+..-.|.|+||..||..-+. ..||+|+.+.-..|.
T Consensus 7 lLrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 7 LLRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDI 55 (65)
T ss_dssp TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-
T ss_pred hcCCcHHHHHhcC--CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHH
Confidence 3679999999882 344456999999999988443 459999887655553
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=2.1e-05 Score=78.01 Aligned_cols=47 Identities=30% Similarity=0.922 Sum_probs=35.5
Q ss_pred cccccccccccCCceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955 283 VCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRFELP 329 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~~l~ 329 (363)
.|.||.+-+...+.+..+. |||+||..|+..|+..- ..||+||..++
T Consensus 6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~ 56 (465)
T KOG0827|consen 6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ 56 (465)
T ss_pred eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence 5999955554444555555 99999999999999863 37999994443
No 49
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.60 E-value=2.2e-05 Score=79.16 Aligned_cols=48 Identities=27% Similarity=0.861 Sum_probs=37.4
Q ss_pred ccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 280 ETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
+--+|||||+-+...- .+....|.|.||..|+.+|. ..+||+||.-..
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 3467999999987543 23444599999999999995 458999998665
No 50
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.53 E-value=2.4e-05 Score=77.75 Aligned_cols=51 Identities=35% Similarity=0.893 Sum_probs=42.9
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhc--CCCCCCcCcCCCCCChhH
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS--RNTCPVCRFELPTDDPEY 335 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~--~~sCPlCR~~l~~~d~~~ 335 (363)
..|-||-+.-+ .+++-||||..|..|+..|-.. .++||.||.+|....+..
T Consensus 370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi 422 (563)
T KOG1785|consen 370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI 422 (563)
T ss_pred HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence 46999998755 7889999999999999999744 579999999998776543
No 51
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=8.4e-05 Score=74.25 Aligned_cols=49 Identities=31% Similarity=0.812 Sum_probs=38.4
Q ss_pred cccccccccccc--cCCceEEeCCCCcccHhhHHHHHhc--CCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVN--VGETATKLPCGHVYHGDCIVPWLDS--RNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~--~~e~~~~LPC~H~Fh~~CI~~WLk~--~~sCPlCR~~l~ 329 (363)
...|+|||+.+. ....+..+.|+|.|...||.+||-+ +..||.|..+-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 467999999876 3345666779999999999999953 347999976543
No 52
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=6.7e-05 Score=80.04 Aligned_cols=50 Identities=28% Similarity=0.778 Sum_probs=41.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d 332 (363)
.-..|++|-.-++ .+++..|+|.||..||..-+..+ ..||.|...|...|
T Consensus 642 ~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 642 ELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred hceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 3478999998877 45667799999999999999765 58999999987655
No 53
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.28 E-value=5.8e-05 Score=73.63 Aligned_cols=53 Identities=25% Similarity=0.598 Sum_probs=42.3
Q ss_pred cccccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 277 SEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 277 ~~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
.......|.+|...|.. .-++.-|-|.||++||.+.|...++||.|...|...
T Consensus 11 ~~n~~itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 11 ELNPHITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred hcccceehhhccceeec--chhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 33456789999998873 233334999999999999999999999998877544
No 54
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.15 E-value=0.00028 Score=71.44 Aligned_cols=50 Identities=30% Similarity=0.715 Sum_probs=44.0
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
.+..|.||+..+. .++.+||||.||..||.+-+-....||+||..+..-.
T Consensus 83 sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~~ 132 (398)
T KOG4159|consen 83 SEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVELP 132 (398)
T ss_pred chhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCcccccccccch
Confidence 4578999999887 6778899999999999998888889999999998733
No 55
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.08 E-value=0.0003 Score=52.25 Aligned_cols=42 Identities=21% Similarity=0.665 Sum_probs=28.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--CCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--NTCPV 323 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--~sCPl 323 (363)
....|||.+..|. +.++-..|+|+|-+..|.+||+++ ..||+
T Consensus 10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4578999999988 355556799999999999999543 37998
No 56
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.07 E-value=0.00021 Score=72.41 Aligned_cols=52 Identities=31% Similarity=0.809 Sum_probs=43.8
Q ss_pred ccccccccccccccCCceEE-eCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955 280 ETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE 334 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~-LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~ 334 (363)
....|+||+..+. .+.. ..|+|.||..||.+|+..+..||.||..+......
T Consensus 20 ~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 20 ENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred ccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 5688999999988 4445 57999999999999999999999999887655443
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.01 E-value=0.0002 Score=71.26 Aligned_cols=47 Identities=30% Similarity=0.893 Sum_probs=38.7
Q ss_pred ccccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCC--CCCCcCc
Q 017955 280 ETIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRF 326 (363)
Q Consensus 280 ~~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlCR~ 326 (363)
....|..|-+.+... +..-.|||.||||..|+...|.++. +||.||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 457799998877643 4677899999999999999997754 8999993
No 58
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00014 Score=53.14 Aligned_cols=46 Identities=24% Similarity=0.561 Sum_probs=35.1
Q ss_pred ccccccccccccCCceEEeCCCC-cccHhhHHHHHh-cCCCCCCcCcCCCC
Q 017955 282 IVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLD-SRNTCPVCRFELPT 330 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk-~~~sCPlCR~~l~~ 330 (363)
..|.||++.-. .-+...||| -.|..|-.+-++ .+..||+||.++..
T Consensus 8 dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 8 DECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD 55 (62)
T ss_pred cceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence 67999999744 233456999 578999777666 78899999998753
No 59
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.73 E-value=0.00084 Score=61.42 Aligned_cols=51 Identities=22% Similarity=0.460 Sum_probs=42.9
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE 334 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~ 334 (363)
-..|.||..+|. .++...|||.||..|...-++....|-+|-+....--++
T Consensus 196 PF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V 246 (259)
T COG5152 196 PFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWV 246 (259)
T ss_pred ceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhccceeH
Confidence 357999999998 677788999999999999999999999998766554443
No 60
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.52 E-value=0.0012 Score=63.68 Aligned_cols=54 Identities=20% Similarity=0.391 Sum_probs=45.4
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHH
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEE 338 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~ 338 (363)
..|-||...|. .++...|+|+||..|...-++....|++|-+.+..-.....+.
T Consensus 242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL 295 (313)
T KOG1813|consen 242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKEL 295 (313)
T ss_pred ccccccccccc---cchhhcCCceeehhhhccccccCCcceecccccccccchHHHH
Confidence 45999999998 6778889999999999999999999999998887655444433
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.50 E-value=0.0015 Score=73.53 Aligned_cols=52 Identities=27% Similarity=0.641 Sum_probs=43.1
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----------CCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----------TCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----------sCPlCR~~l~~~ 331 (363)
.+..|.||+-+--.....++|.|+|+||..|...-|.++- +||+|+.+|...
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence 5678999998766666788999999999999998887642 799999988653
No 62
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.42 E-value=0.0015 Score=65.62 Aligned_cols=46 Identities=24% Similarity=0.551 Sum_probs=38.2
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--------CCCCCcCc
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--------NTCPVCRF 326 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--------~sCPlCR~ 326 (363)
-..|.||++....++....|||+|+||+.|++.++... -.||-+.-
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 36799999999877899999999999999999998642 26877643
No 63
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.42 E-value=0.0023 Score=45.63 Aligned_cols=40 Identities=28% Similarity=0.801 Sum_probs=27.3
Q ss_pred ccccccccccCCceEEeCC--CC---cccHhhHHHHHhc--CCCCCCc
Q 017955 284 CAICKDTVNVGETATKLPC--GH---VYHGDCIVPWLDS--RNTCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC--~H---~Fh~~CI~~WLk~--~~sCPlC 324 (363)
|-||++.-.... ..+.|| +- +.|..||..|+.. +.+|++|
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 779999866443 566785 33 8899999999974 4579988
No 64
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.27 E-value=0.0078 Score=57.74 Aligned_cols=91 Identities=18% Similarity=0.384 Sum_probs=57.8
Q ss_pred hHHHHHHHHHHhcCCCCCCCh-hhHHHHHcCCceeeec--------------ccccccccccccccccCCc-eEEeCCCC
Q 017955 241 GYEALLQNLAESDGGRRGAPR-AAKSAVLELPTVEILS--------------EQETIVCAICKDTVNVGET-ATKLPCGH 304 (363)
Q Consensus 241 ~~e~Ll~~L~~~~~~~~~~~~-~s~~~i~~lp~~~~~~--------------~~~~~~C~ICle~f~~~e~-~~~LPC~H 304 (363)
+.+.||..|............ .-...+..+..+.+.. ......|||....|..... +...||||
T Consensus 58 nKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~ 137 (260)
T PF04641_consen 58 NKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGC 137 (260)
T ss_pred cHHHHHHHHHhcCcCCCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCC
Confidence 577888888766422111111 1112233333444332 2356789999999965443 55558999
Q ss_pred cccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 305 VYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 305 ~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
+|...+|.+- +....||+|-.+|...|
T Consensus 138 V~s~~alke~-k~~~~Cp~c~~~f~~~D 164 (260)
T PF04641_consen 138 VFSEKALKEL-KKSKKCPVCGKPFTEED 164 (260)
T ss_pred EeeHHHHHhh-cccccccccCCccccCC
Confidence 9999999987 33568999999987665
No 65
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.20 E-value=0.0044 Score=59.38 Aligned_cols=49 Identities=24% Similarity=0.534 Sum_probs=37.5
Q ss_pred cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--CCCCCcCcCCC
Q 017955 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--NTCPVCRFELP 329 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--~sCPlCR~~l~ 329 (363)
..+.+|++|-+.-.. .-...+|+|+||..||..-+... -+||.|-..+.
T Consensus 237 t~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 366889999987552 33445699999999999876543 58999988765
No 66
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.16 E-value=0.0021 Score=66.27 Aligned_cols=56 Identities=30% Similarity=0.647 Sum_probs=44.3
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-----CCCCCCcCcCCCCCChhHHHH
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-----RNTCPVCRFELPTDDPEYEEE 338 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-----~~sCPlCR~~l~~~d~~~~~~ 338 (363)
....|.+|.+.-. ..+...|.|.||+.||+++... +-+||+|-..+.-+.....-.
T Consensus 535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~ale 595 (791)
T KOG1002|consen 535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALE 595 (791)
T ss_pred CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhh
Confidence 5677999998755 5566779999999999999753 348999999888776665544
No 67
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.14 E-value=0.0033 Score=45.05 Aligned_cols=45 Identities=22% Similarity=0.560 Sum_probs=22.8
Q ss_pred cccccccccc-CCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCC
Q 017955 284 CAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFEL 328 (363)
Q Consensus 284 C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l 328 (363)
|++|.+.+.. +.....-+|++.+|+.|...-++. ...||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7999999843 224444458999999998887764 67999999864
No 68
>PHA03096 p28-like protein; Provisional
Probab=96.04 E-value=0.003 Score=61.41 Aligned_cols=45 Identities=24% Similarity=0.475 Sum_probs=32.3
Q ss_pred ccccccccccccC----CceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCc
Q 017955 282 IVCAICKDTVNVG----ETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRF 326 (363)
Q Consensus 282 ~~C~ICle~f~~~----e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~ 326 (363)
..|.||++..... ..-..|+ |.|.||..||..|-..+ .+||.||.
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 5699999976632 2445666 99999999999997653 24555543
No 69
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.92 E-value=0.0043 Score=60.06 Aligned_cols=42 Identities=31% Similarity=0.768 Sum_probs=34.5
Q ss_pred ccccccccccccCCceEEeC-CCCcccHhhHHHHHhcC-CCCCCcCc
Q 017955 282 IVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR-NTCPVCRF 326 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~-~sCPlCR~ 326 (363)
+.|+.|...+. .+.+.| |+|.||..||..-|... ..||.|-+
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 78999998877 566677 89999999999887654 58999944
No 70
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0039 Score=61.62 Aligned_cols=49 Identities=27% Similarity=0.459 Sum_probs=42.2
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
++..|+||+-.-. ..+..||+|.-|+.||.+.|.+.+.|=.|+..+.+.
T Consensus 421 Ed~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 421 EDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV 469 (489)
T ss_pred ccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence 6778999987533 567789999999999999999999999999988753
No 71
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.80 E-value=0.0032 Score=62.33 Aligned_cols=46 Identities=33% Similarity=0.712 Sum_probs=34.6
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
....|.||++... ...-+||||.-| |+.--. ...+||+||..+.-.
T Consensus 304 ~p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~~~ 349 (355)
T KOG1571|consen 304 QPDLCVVCLDEPK---SAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIRLV 349 (355)
T ss_pred CCCceEEecCCcc---ceeeecCCcEEE--chHHHh-hCCCCchhHHHHHHH
Confidence 3467999999987 478899999877 765543 344599999877543
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.77 E-value=0.0052 Score=66.56 Aligned_cols=70 Identities=26% Similarity=0.434 Sum_probs=44.8
Q ss_pred ccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCC-------CCCCcCcCCCCCChhHHHHHHhhhccCCCC
Q 017955 280 ETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRN-------TCPVCRFELPTDDPEYEEERKKRVSAGASV 349 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~-------sCPlCR~~l~~~d~~~~~~~~~~~~~~~~~ 349 (363)
....|.||++.+.... ....-.|-|+||+.||.+|.+... .||.|.....+-...|-=+=.+..-|...+
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~~y~C~CGk~~nP~~~~ 267 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPKTYLCFCGKVKNPEFSR 267 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCCcccceecCcccCCCCCC
Confidence 4577999999987433 333334899999999999986522 699998544333334443334444444433
No 73
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=95.60 E-value=0.0041 Score=63.18 Aligned_cols=10 Identities=20% Similarity=0.238 Sum_probs=4.4
Q ss_pred HHHHHHHHhc
Q 017955 244 ALLQNLAESD 253 (363)
Q Consensus 244 ~Ll~~L~~~~ 253 (363)
+.|..|....
T Consensus 209 AY~Scle~Rr 218 (458)
T PF10446_consen 209 AYISCLEARR 218 (458)
T ss_pred HHHHHHHHHH
Confidence 3444444433
No 74
>PHA02862 5L protein; Provisional
Probab=95.60 E-value=0.0086 Score=52.38 Aligned_cols=45 Identities=27% Similarity=0.721 Sum_probs=33.9
Q ss_pred ccccccccccccCCceEEeCCC-----CcccHhhHHHHHhcC--CCCCCcCcCCCC
Q 017955 282 IVCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSR--NTCPVCRFELPT 330 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~--~sCPlCR~~l~~ 330 (363)
..|-||++.-.. . .-||. ..-|..|+.+|++.+ .+||+|+.++..
T Consensus 3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 569999997542 2 24553 578999999999754 489999998753
No 75
>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=95.59 E-value=0.0074 Score=52.23 Aligned_cols=44 Identities=27% Similarity=0.601 Sum_probs=33.4
Q ss_pred cccccccccccccCCceEEeCCC------CcccHhhHHHHHhcCCCCCCc
Q 017955 281 TIVCAICKDTVNVGETATKLPCG------HVYHGDCIVPWLDSRNTCPVC 324 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~------H~Fh~~CI~~WLk~~~sCPlC 324 (363)
...|.||++.+.....++.++|+ |.||..|+++|-+.++.=|.=
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfn 75 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFN 75 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCcc
Confidence 45699999999874567777886 899999999995544444443
No 76
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.54 E-value=0.0041 Score=55.31 Aligned_cols=29 Identities=34% Similarity=0.855 Sum_probs=26.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccH
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHG 308 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~ 308 (363)
..-.|.|||+++..++.+.+|||-.|||+
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEeec
Confidence 45679999999999999999999999996
No 77
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.48 E-value=0.011 Score=58.27 Aligned_cols=46 Identities=35% Similarity=0.816 Sum_probs=38.9
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHH--HhcCCCCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPW--LDSRNTCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~W--Lk~~~sCPlCR~~l 328 (363)
+...|.||-..+. ....+||+|..|..|.... |-..+.||+||.+.
T Consensus 60 en~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 60 ENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 5567999999877 6789999999999998764 56788999999864
No 78
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.46 E-value=0.014 Score=56.54 Aligned_cols=51 Identities=27% Similarity=0.615 Sum_probs=40.7
Q ss_pred ccccccccccccC---CceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955 282 IVCAICKDTVNVG---ETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD 332 (363)
Q Consensus 282 ~~C~ICle~f~~~---e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d 332 (363)
..|-||-++|... ..++.|.|||.||..|+.+-+.... .||.||.......
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~ 58 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTEIPD 58 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcccCCc
Confidence 4699999999865 3677888999999999987776644 7999999854333
No 79
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.0032 Score=60.78 Aligned_cols=41 Identities=39% Similarity=0.794 Sum_probs=32.7
Q ss_pred cccccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFEL 328 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l 328 (363)
...|.|||+.-. ....|+||| +-|..|-+. -+.||+||+.|
T Consensus 300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKR----MNECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCc---ceEEeecCcEEeehhhccc----cccCchHHHHH
Confidence 467999999866 677899999 678888644 34899999855
No 80
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.22 E-value=0.013 Score=52.01 Aligned_cols=48 Identities=23% Similarity=0.662 Sum_probs=35.0
Q ss_pred ccccccccccccccCCceEEeCC--CC---cccHhhHHHHHhcC--CCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPC--GH---VYHGDCIVPWLDSR--NTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC--~H---~Fh~~CI~~WLk~~--~sCPlCR~~l~~~ 331 (363)
....|-||++... .. .-|| .. .-|.+|+..|+..+ .+|++|+.++...
T Consensus 7 ~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 4567999998743 22 2464 44 66999999999764 4899999877543
No 81
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.20 E-value=0.018 Score=54.46 Aligned_cols=58 Identities=22% Similarity=0.381 Sum_probs=48.0
Q ss_pred ccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHH
Q 017955 280 ETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEE 337 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~ 337 (363)
....|+||.+.+...-....| ||||+|++.|+.+.++.-..||+|-.++...|....+
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence 346799999998865544444 6999999999999999999999999999998876543
No 82
>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=95.20 E-value=0.0088 Score=48.74 Aligned_cols=32 Identities=34% Similarity=0.812 Sum_probs=27.1
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHH
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIV 312 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~ 312 (363)
....|+||...+.. ......||+|+||..|+.
T Consensus 77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 45679999998875 477788999999999975
No 83
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.02 Score=56.23 Aligned_cols=46 Identities=26% Similarity=0.591 Sum_probs=36.8
Q ss_pred ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l 328 (363)
....|+||+.... .++.+. -|-+||..||..++++++.||+=-.+.
T Consensus 299 ~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred ccccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 5678999998755 344444 599999999999999999999865544
No 84
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.98 E-value=0.013 Score=43.15 Aligned_cols=47 Identities=36% Similarity=0.805 Sum_probs=34.9
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~ 333 (363)
..|..|... +.+...+||+|+.|..|.. +.+-+.||+|-++|...++
T Consensus 8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~--~~rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 8 QPCVFCGFV---GTKGTVLPCGHLICDNCFP--GERYNGCPFCGTPFEFDDP 54 (55)
T ss_pred eeEEEcccc---ccccccccccceeeccccC--hhhccCCCCCCCcccCCCC
Confidence 345555544 3367889999999999954 3567789999999987664
No 85
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=94.90 E-value=0.022 Score=62.36 Aligned_cols=13 Identities=23% Similarity=0.371 Sum_probs=7.0
Q ss_pred CCceecccCCCCc
Q 017955 41 LPDVICHECKNGF 53 (363)
Q Consensus 41 ~~~~~c~~C~~gF 53 (363)
..||-|++=+.-|
T Consensus 1326 ~sdvh~~r~k~p~ 1338 (1516)
T KOG1832|consen 1326 MSDVHTRRVKHPL 1338 (1516)
T ss_pred hhhhcccccccch
Confidence 4556666655443
No 86
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.78 E-value=0.019 Score=55.56 Aligned_cols=57 Identities=28% Similarity=0.549 Sum_probs=44.1
Q ss_pred ccccccccccccc-CCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHH
Q 017955 281 TIVCAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEE 338 (363)
Q Consensus 281 ~~~C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~ 338 (363)
...||||.+.+.. ...+..++|+|+-|..|+.+....+-+||+|.+ +......+...
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~ 215 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKL 215 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHH
Confidence 3449999997664 347888999999999999999888899999988 55554444333
No 87
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.72 E-value=0.01 Score=55.97 Aligned_cols=46 Identities=20% Similarity=0.533 Sum_probs=34.0
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
..|..|..--. +.....+.|.|+||..|...-. ...||+||+.+..
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRI 49 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeee
Confidence 35777776444 6677788899999999976532 2389999998654
No 88
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.68 E-value=0.0031 Score=62.92 Aligned_cols=57 Identities=28% Similarity=0.631 Sum_probs=46.3
Q ss_pred cccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHH
Q 017955 281 TIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEE 337 (363)
Q Consensus 281 ~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~ 337 (363)
...|.||...++.. +.+..+-|+|++|..||.+||.....||.||+.|+-.-.+.+.
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~~e~k~ 253 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNGFEEKL 253 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhhHHHHH
Confidence 46799999988744 3566677999999999999999999999999999765544443
No 89
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=94.67 E-value=0.024 Score=62.44 Aligned_cols=7 Identities=29% Similarity=0.140 Sum_probs=2.5
Q ss_pred hhhHHHH
Q 017955 239 AAGYEAL 245 (363)
Q Consensus 239 ~~~~e~L 245 (363)
...+.+|
T Consensus 731 De~m~~l 737 (784)
T PF04931_consen 731 DEQMMAL 737 (784)
T ss_pred HHHHHHH
Confidence 3333333
No 90
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=94.54 E-value=0.026 Score=47.77 Aligned_cols=35 Identities=26% Similarity=0.570 Sum_probs=29.4
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+..+||..|. ..+.+...++.||.|++..++=+.
T Consensus 67 ~p~~~~C~~C~----~~~~~e~~~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 67 EPAECWCLDCG----QEVELEELDYRCPKCGSINLRIIG 101 (115)
T ss_pred eccEEEeccCC----CeecchhheeECCCCCCCceEEec
Confidence 46789999999 777777788999999999887664
No 91
>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=94.54 E-value=0.044 Score=54.97 Aligned_cols=69 Identities=28% Similarity=0.484 Sum_probs=41.2
Q ss_pred HHHHHcCCceeee-ccccccccccccccccc-------------CC----ceEEeC--CCCcccHhhHHHHHhcC-----
Q 017955 264 KSAVLELPTVEIL-SEQETIVCAICKDTVNV-------------GE----TATKLP--CGHVYHGDCIVPWLDSR----- 318 (363)
Q Consensus 264 ~~~i~~lp~~~~~-~~~~~~~C~ICle~f~~-------------~e----~~~~LP--C~H~Fh~~CI~~WLk~~----- 318 (363)
++.|..-|..... ..++...|.-|+..-.. |. ...+.+ |...+|.+|+-+|+..+
T Consensus 253 ~~~V~~Np~y~~~~~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~ 332 (358)
T PF10272_consen 253 KEQVEQNPRYSYPESGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQH 332 (358)
T ss_pred HHHHHhCCccccCCCccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCC
Confidence 3445555555544 33456678878764321 00 001112 56778999999998532
Q ss_pred --------CCCCCcCcCCCCCC
Q 017955 319 --------NTCPVCRFELPTDD 332 (363)
Q Consensus 319 --------~sCPlCR~~l~~~d 332 (363)
-.||.||+.|+--|
T Consensus 333 ~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 333 PETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred hhhhhcCCCCCCCCcccceeee
Confidence 27999999987543
No 92
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.51 E-value=0.019 Score=56.62 Aligned_cols=56 Identities=21% Similarity=0.528 Sum_probs=40.8
Q ss_pred ccccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCCh
Q 017955 278 EQETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDP 333 (363)
Q Consensus 278 ~~~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~ 333 (363)
+.++.-|+.|++.+...+ .....|||...|.-|....-+. +..||.||+.....+.
T Consensus 11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv 68 (480)
T COG5175 11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENV 68 (480)
T ss_pred ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccce
Confidence 334455999999988554 4556779998888886554433 5689999998776663
No 93
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=94.34 E-value=0.018 Score=40.28 Aligned_cols=41 Identities=32% Similarity=0.865 Sum_probs=23.3
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHhcCC--CCCCc
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlC 324 (363)
|.+|.+....|..-....|+-.+|..|+..+++... .||.|
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 678888777443222223999999999999998766 79988
No 94
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=94.26 E-value=0.015 Score=59.15 Aligned_cols=6 Identities=33% Similarity=0.036 Sum_probs=2.2
Q ss_pred ccccCC
Q 017955 117 IELDGW 122 (363)
Q Consensus 117 ~~~~~~ 122 (363)
||+-+.
T Consensus 38 IRkLge 43 (458)
T PF10446_consen 38 IRKLGE 43 (458)
T ss_pred HhhhhH
Confidence 333333
No 95
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=93.71 E-value=0.019 Score=40.95 Aligned_cols=33 Identities=30% Similarity=0.744 Sum_probs=23.6
Q ss_pred EeCC-CCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 299 KLPC-GHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 299 ~LPC-~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
.+.| .|+.|..|+...|..+..||+|..++|++
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 4457 49999999999999999999999999875
No 96
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.30 E-value=0.053 Score=49.10 Aligned_cols=50 Identities=30% Similarity=0.740 Sum_probs=34.3
Q ss_pred ccccccccccccCC----ceEEeCCCCcccHhhHHHHHhc----C-------CCCCCcCcCCCCC
Q 017955 282 IVCAICKDTVNVGE----TATKLPCGHVYHGDCIVPWLDS----R-------NTCPVCRFELPTD 331 (363)
Q Consensus 282 ~~C~ICle~f~~~e----~~~~LPC~H~Fh~~CI~~WLk~----~-------~sCPlCR~~l~~~ 331 (363)
..|.||+-.--.|. ..--..|+.-||.-|+..||+. + ..||.|-.++.-+
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 45888875433332 2222349999999999999974 1 2699999887544
No 97
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.23 E-value=0.021 Score=61.86 Aligned_cols=48 Identities=27% Similarity=0.599 Sum_probs=39.2
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC--CCCCcCcCCCCCCh
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRFELPTDDP 333 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlCR~~l~~~d~ 333 (363)
..|.||++ .+.+.+.+|+|.||..|+.+-+.... .||+||..+..+..
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 77999999 34778889999999999999886643 69999987765543
No 98
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=92.80 E-value=0.044 Score=53.50 Aligned_cols=43 Identities=28% Similarity=0.693 Sum_probs=30.5
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l 328 (363)
..|--|-..+. -..+.+||+|+||++|... ..-+.||.|-..|
T Consensus 91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred EeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 45666755444 2567789999999999643 4466899996544
No 99
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=92.11 E-value=0.064 Score=60.82 Aligned_cols=45 Identities=31% Similarity=0.699 Sum_probs=37.7
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~ 327 (363)
...|.||++.+.. ...+.-|+|.||..|+..|+..+..||+|...
T Consensus 1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence 3579999998873 23455699999999999999999999999743
No 100
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=92.07 E-value=0.18 Score=44.92 Aligned_cols=53 Identities=25% Similarity=0.543 Sum_probs=36.7
Q ss_pred cccccccccccccCCceEEeC------------CC-CcccHhhHHHHHhc------------------------------
Q 017955 281 TIVCAICKDTVNVGETATKLP------------CG-HVYHGDCIVPWLDS------------------------------ 317 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LP------------C~-H~Fh~~CI~~WLk~------------------------------ 317 (363)
+..|+|||+.-. ..+.|- |+ -+-|..||.++-|.
T Consensus 2 d~~CpICme~PH---NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (162)
T PF07800_consen 2 DVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ 78 (162)
T ss_pred CccCceeccCCC---ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence 457999999754 344443 33 24678899988541
Q ss_pred -CCCCCCcCcCCCCCChhHH
Q 017955 318 -RNTCPVCRFELPTDDPEYE 336 (363)
Q Consensus 318 -~~sCPlCR~~l~~~d~~~~ 336 (363)
.-.||+||..|..+.....
T Consensus 79 ~~L~CPLCRG~V~GWtvve~ 98 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVEP 98 (162)
T ss_pred ccccCccccCceeceEEchH
Confidence 1169999999998877654
No 101
>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=91.93 E-value=0.12 Score=43.70 Aligned_cols=35 Identities=20% Similarity=0.505 Sum_probs=25.6
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+.++||..|.+.+.. .-..+.||.|++..++-+.
T Consensus 67 ~p~~~~C~~Cg~~~~~----~~~~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 67 EPVECECEDCSEEVSP----EIDLYRCPKCHGIMLQVRA 101 (115)
T ss_pred eCcEEEcccCCCEEec----CCcCccCcCCcCCCcEEec
Confidence 5779999999944443 3335889999998766543
No 102
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=91.09 E-value=0.16 Score=42.87 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=25.0
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+.++||..|...+ ...-..+.||.|++.-++-+.
T Consensus 67 vp~~~~C~~Cg~~~----~~~~~~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 67 KPAQAWCWDCSQVV----EIHQHDAQCPHCHGERLRVDT 101 (113)
T ss_pred eCcEEEcccCCCEE----ecCCcCccCcCCCCCCcEEcc
Confidence 46799999999443 333345679999988766543
No 103
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.88 E-value=0.17 Score=43.38 Aligned_cols=38 Identities=16% Similarity=0.274 Sum_probs=26.0
Q ss_pred CCCceeeeecCCcceee---eccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIE---TLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~---~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+.++|| .|...+... +....+.+.||.|++..++-+.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 5779999 999665543 1112245679999998876553
No 104
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=90.86 E-value=0.076 Score=44.67 Aligned_cols=35 Identities=29% Similarity=0.450 Sum_probs=22.5
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
.+.++||..|. .+..+.-..+.||.|++..++-+.
T Consensus 67 ~p~~~~C~~Cg----~~~~~~~~~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 67 VPARARCRDCG----HEFEPDEFDFSCPRCGSPDVEIIS 101 (113)
T ss_dssp E--EEEETTTS-----EEECHHCCHH-SSSSSS-EEEEE
T ss_pred cCCcEECCCCC----CEEecCCCCCCCcCCcCCCcEEcc
Confidence 46799999999 554444445889999999876543
No 105
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.69 E-value=0.11 Score=48.48 Aligned_cols=40 Identities=33% Similarity=0.722 Sum_probs=30.6
Q ss_pred ccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 284 CAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
|-+|.+.=. .+..+||.| .+|..|=.. ...||+|+.....
T Consensus 161 Cr~C~~~~~---~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGEREA---TVLLLPCRHLCLCGICDES----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcCCc---eEEeecccceEeccccccc----CccCCCCcChhhc
Confidence 888877643 788999998 789999643 4569999886543
No 106
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.56 E-value=0.13 Score=56.08 Aligned_cols=46 Identities=33% Similarity=0.825 Sum_probs=35.1
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
....|.+|--.+.. ..+..-|+|.||..|+. .....||-|+..+..
T Consensus 839 q~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~~ 884 (933)
T KOG2114|consen 839 QVSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELRG 884 (933)
T ss_pred eeeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhhh
Confidence 34679999887763 45566799999999997 455689999885543
No 107
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.48 E-value=0.22 Score=50.25 Aligned_cols=49 Identities=24% Similarity=0.553 Sum_probs=41.1
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC---CCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~---sCPlCR~~l 328 (363)
..-.|||=.+.-.....+..|.|||+.+++-|.+..++.. .||.|-...
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 4567999888877777899999999999999999888765 799995543
No 108
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.45 E-value=0.15 Score=55.08 Aligned_cols=28 Identities=32% Similarity=0.864 Sum_probs=24.4
Q ss_pred ceEEeCCCCcccHhhHHHHHhcCCCCCC
Q 017955 296 TATKLPCGHVYHGDCIVPWLDSRNTCPV 323 (363)
Q Consensus 296 ~~~~LPC~H~Fh~~CI~~WLk~~~sCPl 323 (363)
...+..|+|+-|.+|.++|+.....||.
T Consensus 1042 s~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1042 SNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred chhhccccccccHHHHHHHHhcCCcCCC
Confidence 3455679999999999999999999985
No 109
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.40 E-value=0.22 Score=54.94 Aligned_cols=11 Identities=9% Similarity=-0.018 Sum_probs=4.1
Q ss_pred ccccCCCcccc
Q 017955 117 IELDGWENDAR 127 (363)
Q Consensus 117 ~~~~~~~~~~~ 127 (363)
.|.+..+++++
T Consensus 1400 ~r~~~dd~Dee 1410 (1516)
T KOG1832|consen 1400 RRPTDDDSDEE 1410 (1516)
T ss_pred cCCCccccCcc
Confidence 33333333333
No 110
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.36 E-value=0.26 Score=36.20 Aligned_cols=33 Identities=30% Similarity=0.738 Sum_probs=27.8
Q ss_pred cccccccccccccCCceEEeC-CCCcccHhhHHH
Q 017955 281 TIVCAICKDTVNVGETATKLP-CGHVYHGDCIVP 313 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~ 313 (363)
...|++|-+.|+.++.+++-| |+-.||+.|..+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 457999999998777777787 999999999543
No 111
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=90.31 E-value=0.2 Score=42.29 Aligned_cols=36 Identities=19% Similarity=0.636 Sum_probs=24.8
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+.++||..|...+..... .-+.||.|++..++-+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~---~~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQ---RVRRCPQCHGDMLRIVA 102 (114)
T ss_pred eCcEEEcccCCCeeecCCc---cCCcCcCcCCCCcEEcc
Confidence 5779999999954443211 12569999988776554
No 112
>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=89.48 E-value=0.72 Score=38.67 Aligned_cols=34 Identities=21% Similarity=0.430 Sum_probs=25.4
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
+.+.-|..|.++|- .++-.-+|||+|+.-|.-+.
T Consensus 7 GtKR~Cp~CG~kFY---DLnk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 7 GTKRTCPSCGAKFY---DLNKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred CCcccCCCCcchhc---cCCCCCccCCCCCCccCccc
Confidence 45788999996664 34444588999999997773
No 113
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=89.20 E-value=0.38 Score=47.32 Aligned_cols=53 Identities=23% Similarity=0.606 Sum_probs=38.5
Q ss_pred ccccccccccccccCCceEEeCC--CCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHHHH
Q 017955 280 ETIVCAICKDTVNVGETATKLPC--GHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERK 340 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC--~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~~~ 340 (363)
.-..||||.+.+.. -++.| ||+-|..|-. +.++.||.||.++. +-..+.-++.
T Consensus 47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g-~~R~~amEkV 101 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG-NIRCRAMEKV 101 (299)
T ss_pred hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCccccccc-cHHHHHHHHH
Confidence 44679999999872 34557 7999988864 56889999999998 4444444433
No 114
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.84 E-value=0.27 Score=41.68 Aligned_cols=35 Identities=17% Similarity=0.420 Sum_probs=24.4
Q ss_pred CCCceeeeecCCcceeeeccCCCce-ecccCCCCceeecc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDV-ICHECKNGFVESIP 58 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~-~c~~C~~gFve~~~ 58 (363)
-+.++||..|...+... -..+ .||.|++-.++-+.
T Consensus 68 vp~~~~C~~Cg~~~~~~----~~~~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 68 EKVELECKDCSHVFKPN----ALDYGVCEKCHSKNVIITQ 103 (117)
T ss_pred cCCEEEhhhCCCccccC----CccCCcCcCCCCCceEEec
Confidence 57799999999444332 2234 49999998877553
No 115
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=88.70 E-value=0.32 Score=42.12 Aligned_cols=56 Identities=21% Similarity=0.474 Sum_probs=41.0
Q ss_pred ccccccccccccccccCCceEEeC-CCCcccHhhHHHHHhc---CCCCCCcCcCCCCCCh
Q 017955 278 EQETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDS---RNTCPVCRFELPTDDP 333 (363)
Q Consensus 278 ~~~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~---~~sCPlCR~~l~~~d~ 333 (363)
+..-.+|.||.+......-.+.=- ||-..|..|....+|. +..||+|+..+.....
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 336678999999876433222222 8999999998888775 5589999999976553
No 116
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=88.63 E-value=0.25 Score=35.60 Aligned_cols=31 Identities=23% Similarity=0.563 Sum_probs=24.9
Q ss_pred CceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 22 TQYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 22 ~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
.-|-|-.|.+.| +.+-..+.+-||+|++--+
T Consensus 5 ~~Y~C~~Cg~~~--~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 5 MEYKCARCGREV--ELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred EEEEhhhcCCee--ehhhccCceeCCCCCcEEE
Confidence 469999999777 5566778999999997543
No 117
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=88.55 E-value=0.25 Score=50.40 Aligned_cols=35 Identities=26% Similarity=0.543 Sum_probs=30.2
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS 317 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~ 317 (363)
+...|+||..-|. .+++|||+|..|..|...-+.+
T Consensus 3 eelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYR---EPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhcc---CceEeecccHHHHHHHHhhccc
Confidence 4578999999887 7899999999999999876654
No 118
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.70 E-value=0.33 Score=53.45 Aligned_cols=37 Identities=24% Similarity=0.654 Sum_probs=29.7
Q ss_pred cccccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD 316 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk 316 (363)
.....|.||...+... .-.+.||+|.||++||.+-..
T Consensus 815 ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cCccchHHhcchhhcC-cceeeeccchHHHHHHHHHHH
Confidence 3567899999887653 566789999999999988743
No 119
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.43 E-value=0.45 Score=48.36 Aligned_cols=39 Identities=23% Similarity=0.536 Sum_probs=28.6
Q ss_pred ccccccccccccccC-CceEEeCCCCcccHhhHHHHHhcC
Q 017955 280 ETIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSR 318 (363)
Q Consensus 280 ~~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~ 318 (363)
....|.||+..+... .....+.|+|.||..|+++.+..+
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~ 184 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK 184 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence 467899999544433 333455699999999999988743
No 120
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.22 E-value=0.28 Score=47.70 Aligned_cols=31 Identities=23% Similarity=0.641 Sum_probs=24.6
Q ss_pred CCCcccHhhHHHHHh-------------cCCCCCCcCcCCCCCC
Q 017955 302 CGHVYHGDCIVPWLD-------------SRNTCPVCRFELPTDD 332 (363)
Q Consensus 302 C~H~Fh~~CI~~WLk-------------~~~sCPlCR~~l~~~d 332 (363)
|...+|.+|+-+|+. ++-+||.||+.++--|
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 677899999999974 2448999999987544
No 121
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.97 E-value=0.44 Score=41.40 Aligned_cols=39 Identities=15% Similarity=0.398 Sum_probs=26.2
Q ss_pred CCCCceeeeecCCcceeee---------------ccC--CCceecccCCCCceeec
Q 017955 19 TDPTQYWCHHCEKRVSIET---------------LAN--LPDVICHECKNGFVESI 57 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~---------------~~~--~~~~~c~~C~~gFve~~ 57 (363)
..+.+|||..|...+...- .|. ...+.||+|++.-++-+
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 3568999999997666641 010 23466999998766544
No 122
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=84.99 E-value=0.6 Score=44.79 Aligned_cols=7 Identities=29% Similarity=1.260 Sum_probs=2.9
Q ss_pred eeeeecC
Q 017955 24 YWCHHCE 30 (363)
Q Consensus 24 ~~C~~C~ 30 (363)
|.|-.|+
T Consensus 172 ~KC~SCN 178 (314)
T PF06524_consen 172 FKCQSCN 178 (314)
T ss_pred ccccccc
Confidence 4444443
No 123
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=84.69 E-value=0.66 Score=44.50 Aligned_cols=10 Identities=40% Similarity=0.800 Sum_probs=4.9
Q ss_pred eeeecCCcce
Q 017955 25 WCHHCEKRVS 34 (363)
Q Consensus 25 ~C~~C~~~~~ 34 (363)
-|..|.+.||
T Consensus 127 ~C~EC~R~vw 136 (314)
T PF06524_consen 127 VCIECERGVW 136 (314)
T ss_pred Eeeeeecccc
Confidence 4555554444
No 124
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=84.67 E-value=0.43 Score=46.10 Aligned_cols=51 Identities=22% Similarity=0.576 Sum_probs=36.9
Q ss_pred cccccccccccccCCc-eEEeCCC-----CcccHhhHHHHHh--cCCCCCCcCcCCCCC
Q 017955 281 TIVCAICKDTVNVGET-ATKLPCG-----HVYHGDCIVPWLD--SRNTCPVCRFELPTD 331 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~-~~~LPC~-----H~Fh~~CI~~WLk--~~~sCPlCR~~l~~~ 331 (363)
...|-||+........ ....||. ++.|..|+..|+. .+..|.+|...+...
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 4679999997653211 4567763 6789999999997 455899998865443
No 125
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=83.97 E-value=0.25 Score=53.26 Aligned_cols=46 Identities=24% Similarity=0.758 Sum_probs=36.5
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR---NTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~---~sCPlCR~~l~ 329 (363)
...|+||+..+. .+..+.|.|+|+..|+..-|... ..||+|+..+.
T Consensus 21 ~lEc~ic~~~~~---~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 21 ILECPICLEHVK---EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hccCCceeEEee---ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 467999999988 45678899999999987766443 47999986554
No 126
>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=83.83 E-value=0.86 Score=44.31 Aligned_cols=47 Identities=23% Similarity=0.509 Sum_probs=33.8
Q ss_pred cccccccccccCC--ceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCC
Q 017955 283 VCAICKDTVNVGE--TATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELP 329 (363)
Q Consensus 283 ~C~ICle~f~~~e--~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~ 329 (363)
.|++|.-...... ...+-+|+|..|.+|+...+... ..||.|-+.+-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 4999987544322 23333799999999999988654 48999977654
No 127
>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=83.81 E-value=1.3 Score=31.89 Aligned_cols=43 Identities=21% Similarity=0.566 Sum_probs=19.8
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhc---CC--CCCCcCcC
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS---RN--TCPVCRFE 327 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~---~~--sCPlCR~~ 327 (363)
..|+|.+..+.. .++-..|.|+-|.+ +..||+. .+ .||+|.++
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 569998887762 44445599985543 3455543 22 69999763
No 128
>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=82.29 E-value=1 Score=30.21 Aligned_cols=29 Identities=24% Similarity=0.619 Sum_probs=22.2
Q ss_pred ceeeeecCCcceeeeccC-CCceecccCCC
Q 017955 23 QYWCHHCEKRVSIETLAN-LPDVICHECKN 51 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~-~~~~~c~~C~~ 51 (363)
.|.|..|.+.|.+..... .....||.|++
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 689999998777664322 56688999998
No 129
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.00 E-value=0.55 Score=44.94 Aligned_cols=49 Identities=31% Similarity=0.670 Sum_probs=33.6
Q ss_pred ccccccccccccccCCce-EEeCC-----CCcccHhhHHHHHhcCC--------CCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGETA-TKLPC-----GHVYHGDCIVPWLDSRN--------TCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~-~~LPC-----~H~Fh~~CI~~WLk~~~--------sCPlCR~~l 328 (363)
.+..|-||+..=++.... -.-|| .|-.|..||..|+..++ +||.|+.+.
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 456699999875533221 22355 37899999999985332 699999864
No 130
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=81.48 E-value=1.3 Score=48.26 Aligned_cols=44 Identities=23% Similarity=0.573 Sum_probs=31.6
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCC--cCc
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPV--CRF 326 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPl--CR~ 326 (363)
..|.+|-..+. |..+-+--|+|.-|.+|+++|+..+.-||. |-.
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 36888877655 112222239999999999999999988876 544
No 131
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=81.28 E-value=0.82 Score=50.02 Aligned_cols=52 Identities=23% Similarity=0.716 Sum_probs=38.2
Q ss_pred ccccccccccccccCCceEEeCCC-----CcccHhhHHHHHhcCC--CCCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSRN--TCPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~~--sCPlCR~~l~~~d 332 (363)
++..|-||...=..+ .+..-||+ .+.|.+|+.+|+.-+. .|-+|..++.-++
T Consensus 11 d~~~CRICr~e~~~d-~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 11 DKRSCRICRTEDIRD-DPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD 69 (1175)
T ss_pred cchhceeecCCCCCC-CcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence 457899999865433 33345665 4789999999997644 7999998876554
No 132
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.99 E-value=1 Score=33.93 Aligned_cols=22 Identities=23% Similarity=0.601 Sum_probs=18.0
Q ss_pred cceeeeccCCCceecccCCCCce
Q 017955 32 RVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 32 ~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
+|++++ .+.-+++||||+.-|.
T Consensus 38 rV~L~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 38 RVFLDM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEEEc-CCCCcEecCccccEEE
Confidence 577887 6678999999998774
No 133
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=80.44 E-value=1 Score=48.54 Aligned_cols=18 Identities=11% Similarity=0.253 Sum_probs=11.5
Q ss_pred ccChhhHHHHHHHHHHhc
Q 017955 236 YMDAAGYEALLQNLAESD 253 (363)
Q Consensus 236 ~~~~~~~e~Ll~~L~~~~ 253 (363)
.+....|..++..|....
T Consensus 253 ~i~~~~Y~~~~~~L~~eV 270 (622)
T PF02724_consen 253 RISSERYDRYVPLLQDEV 270 (622)
T ss_pred ccchhhHHHHHHHHHHHH
Confidence 356677777777666544
No 134
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=80.15 E-value=0.62 Score=49.58 Aligned_cols=42 Identities=24% Similarity=0.707 Sum_probs=27.1
Q ss_pred cccccccccc-----ccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCc
Q 017955 280 ETIVCAICKD-----TVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVC 324 (363)
Q Consensus 280 ~~~~C~ICle-----~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlC 324 (363)
....|.||.. .|......++..|+++||..|+. ..+..||.|
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~---r~s~~CPrC 556 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLR---RKSPCCPRC 556 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHh---ccCCCCCch
Confidence 3456788833 23222345556699999999954 344459999
No 135
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=79.30 E-value=1.2 Score=41.54 Aligned_cols=49 Identities=27% Similarity=0.512 Sum_probs=38.3
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
-..|.+|..-.-. .+++-.|+-.||..|+...++....||.|..-+++.
T Consensus 181 lk~Cn~Ch~LvIq--g~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w~h~ 229 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQ--GIRCGSCNIQYHRGCIQTYLQRRDICPHCGDLWTHP 229 (235)
T ss_pred HHHHhHhHHHhhe--eeccCcccchhhhHHHHHHhcccCcCCchhcccCcc
Confidence 3579999987552 344556899999999999999999999996555443
No 136
>PRK07591 threonine synthase; Validated
Probab=79.26 E-value=1.5 Score=45.03 Aligned_cols=32 Identities=19% Similarity=0.391 Sum_probs=20.9
Q ss_pred CCCCceeeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 19 TDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
+.-..+.|..|.+.+. +... +.||.|++ .++-
T Consensus 14 ~~~~~l~C~~Cg~~~~----~~~~-~~C~~cg~-~l~~ 45 (421)
T PRK07591 14 GPAVALKCRECGAEYP----LGPI-HVCEECFG-PLEV 45 (421)
T ss_pred cceeEEEeCCCCCcCC----CCCC-ccCCCCCC-eEEE
Confidence 3445688999994443 3333 89999974 4443
No 137
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=79.04 E-value=2 Score=46.88 Aligned_cols=10 Identities=10% Similarity=-0.071 Sum_probs=5.0
Q ss_pred HHHHHHHhhh
Q 017955 86 QVLRLIAQAA 95 (363)
Q Consensus 86 ~~~~~~~~~~ 95 (363)
.-|.-|-.+.
T Consensus 846 LNW~~ImKTI 855 (960)
T KOG1189|consen 846 LNWTKIMKTI 855 (960)
T ss_pred ccHHHHhhhh
Confidence 3455555544
No 138
>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=78.45 E-value=0.72 Score=43.78 Aligned_cols=47 Identities=23% Similarity=0.508 Sum_probs=34.8
Q ss_pred ccccccccccccccCCceE--EeC-CCCcccHhhHHHHHhcCC-CCC--CcCc
Q 017955 280 ETIVCAICKDTVNVGETAT--KLP-CGHVYHGDCIVPWLDSRN-TCP--VCRF 326 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~--~LP-C~H~Fh~~CI~~WLk~~~-sCP--lCR~ 326 (363)
.+..||||..+-.....++ +-| |-|..|-+|+...|.... .|| -|.+
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 4568999998655433333 336 999999999999997755 799 6744
No 139
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.08 E-value=4.9 Score=38.58 Aligned_cols=50 Identities=20% Similarity=0.399 Sum_probs=37.1
Q ss_pred cccccccccccccCCc-eEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 281 TIVCAICKDTVNVGET-ATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~-~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
...|+|---.|..... ....+|||+|-..-+++. ...+|++|...+..++
T Consensus 111 ~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d 161 (293)
T KOG3113|consen 111 RFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD 161 (293)
T ss_pred eeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence 4579998777764433 445569999998887763 3778999999887766
No 140
>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=75.91 E-value=1.4 Score=29.36 Aligned_cols=32 Identities=16% Similarity=0.373 Sum_probs=23.6
Q ss_pred ceeeeecCCcceeeeccC---CCceecccCCCCce
Q 017955 23 QYWCHHCEKRVSIETLAN---LPDVICHECKNGFV 54 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~---~~~~~c~~C~~gFv 54 (363)
++-|-+|...+.+..... -..+.||.|+.-|.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 356999998887774433 23599999998774
No 141
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.66 E-value=2.7 Score=29.35 Aligned_cols=33 Identities=21% Similarity=0.414 Sum_probs=23.9
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
.|-|-.|...+.. .+....+.||+|++-|+-..
T Consensus 3 ~y~C~~CG~~~~~--~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 3 EYKCARCGREVEL--DEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EEECCCCCCEEEE--CCCCCceECCCCCCeEEEcc
Confidence 5889999955444 34444799999999887543
No 142
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=75.52 E-value=1.5 Score=40.20 Aligned_cols=27 Identities=30% Similarity=0.765 Sum_probs=19.5
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCcee
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
-.-|||-.|+ + .+..-.|+.|+++|-+
T Consensus 12 ~~iyWCe~cN----l----Pl~~~~c~~cg~~~~~ 38 (202)
T COG5270 12 FPIYWCEKCN----L----PLLGRRCSVCGSKVEE 38 (202)
T ss_pred cceeehhhCC----C----ccccccccccCCcceE
Confidence 3569999999 3 3444569999977643
No 143
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=75.41 E-value=1.6 Score=29.03 Aligned_cols=26 Identities=15% Similarity=0.585 Sum_probs=15.2
Q ss_pred eeeecCCcceeeec--cCCCceecccCC
Q 017955 25 WCHHCEKRVSIETL--ANLPDVICHECK 50 (363)
Q Consensus 25 ~C~~C~~~~~~~~~--~~~~~~~c~~C~ 50 (363)
||-.|...+...|. ...+-.+|+.|+
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 79999988888877 556889999996
No 144
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.82 E-value=1.3 Score=47.39 Aligned_cols=40 Identities=30% Similarity=0.778 Sum_probs=30.2
Q ss_pred cccccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCCCCC
Q 017955 281 TIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRNTCP 322 (363)
Q Consensus 281 ~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~sCP 322 (363)
-..|.||+..|..+. .++-|-|+|..|..|+..-. +.+||
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp 51 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP 51 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC
Confidence 356999999887443 56667799999999997754 34666
No 145
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=74.45 E-value=1.7 Score=47.46 Aligned_cols=49 Identities=10% Similarity=0.176 Sum_probs=31.8
Q ss_pred cccccccccccc-CCceEEeC---CCCcccHhhHHHHHhc------CCCCCCcCcCCCC
Q 017955 282 IVCAICKDTVNV-GETATKLP---CGHVYHGDCIVPWLDS------RNTCPVCRFELPT 330 (363)
Q Consensus 282 ~~C~ICle~f~~-~e~~~~LP---C~H~Fh~~CI~~WLk~------~~sCPlCR~~l~~ 330 (363)
..|.||.-.+.. .+....+| |.|.||..||..|+.+ +-.|++|..-|-.
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 345555555543 11233444 9999999999999864 3368888765543
No 146
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.33 E-value=1.5 Score=45.25 Aligned_cols=36 Identities=25% Similarity=0.648 Sum_probs=30.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS 317 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~ 317 (363)
....|.||.+.+.. ....+.|+|.||..|+...+.+
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 45789999999874 5667789999999999998875
No 147
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=73.70 E-value=2.4 Score=48.55 Aligned_cols=10 Identities=20% Similarity=0.076 Sum_probs=4.6
Q ss_pred hHHHHhhhhc
Q 017955 177 EEDLRRRWRD 186 (363)
Q Consensus 177 e~~~rr~~r~ 186 (363)
++++...+|.
T Consensus 1791 egeia~~dRi 1800 (3015)
T KOG0943|consen 1791 EGEIASGDRI 1800 (3015)
T ss_pred ccccccccee
Confidence 3344445553
No 148
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=73.20 E-value=2.5 Score=41.86 Aligned_cols=50 Identities=24% Similarity=0.507 Sum_probs=38.5
Q ss_pred ccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955 282 IVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331 (363)
Q Consensus 282 ~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~ 331 (363)
..|+||.+..... ......||++..|..|+..-...+.+||.||+.....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 6799999977432 2455566899899999988888889999999655443
No 149
>PF14353 CpXC: CpXC protein
Probab=71.58 E-value=2.3 Score=36.10 Aligned_cols=33 Identities=24% Similarity=0.539 Sum_probs=24.2
Q ss_pred eeeecCCcceeeeccC-----------------CCceecccCCCCceeec
Q 017955 25 WCHHCEKRVSIETLAN-----------------LPDVICHECKNGFVESI 57 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~-----------------~~~~~c~~C~~gFve~~ 57 (363)
-|.+|...+..++... +-.++||+|+.-|.=+.
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCC
Confidence 4899998877765443 34799999999986433
No 150
>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=71.30 E-value=4.5 Score=27.86 Aligned_cols=33 Identities=24% Similarity=0.506 Sum_probs=24.0
Q ss_pred ceeeeecCCcceeeeccC-CCceecccCCCCcee
Q 017955 23 QYWCHHCEKRVSIETLAN-LPDVICHECKNGFVE 55 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~-~~~~~c~~C~~gFve 55 (363)
.|-|-.|...|.+...-. ...+.||.|++.=++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 589999997776663322 478999999985444
No 151
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=71.13 E-value=2.2 Score=46.04 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=7.1
Q ss_pred ceeeeecCCcceee
Q 017955 23 QYWCHHCEKRVSIE 36 (363)
Q Consensus 23 ~~~C~~C~~~~~~~ 36 (363)
.+.+-.|...|-+.
T Consensus 54 ~vilIncGa~~dl~ 67 (622)
T PF02724_consen 54 SVILINCGATVDLE 67 (622)
T ss_pred eEEEEecCchhhHH
Confidence 35555555444444
No 152
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.18 E-value=2.4 Score=43.13 Aligned_cols=44 Identities=27% Similarity=0.542 Sum_probs=31.4
Q ss_pred ccccccccccccccCC---ceEEeCCCCcccHhhHHHHHhcCCCCCCc
Q 017955 280 ETIVCAICKDTVNVGE---TATKLPCGHVYHGDCIVPWLDSRNTCPVC 324 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e---~~~~LPC~H~Fh~~CI~~WLk~~~sCPlC 324 (363)
....|++|.-.+.... ..+.- |+|.||+.|...|...+..|..|
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred hcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence 3467888877655322 23333 99999999999998877777554
No 153
>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=68.84 E-value=3.3 Score=28.56 Aligned_cols=30 Identities=23% Similarity=0.585 Sum_probs=22.3
Q ss_pred eeeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
|.|..|.... +..+...-++||+.| |.|-+
T Consensus 1 m~Cp~Cg~~~-~~~D~~~g~~vC~~C--G~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDPERGELVCPNC--GLVLE 30 (43)
T ss_dssp ESBTTTSSSE-EEEETTTTEEEETTT---BBEE
T ss_pred CCCcCCcCCc-eEEcCCCCeEECCCC--CCEee
Confidence 5788998655 667777889999999 55543
No 154
>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=68.62 E-value=4.9 Score=28.54 Aligned_cols=35 Identities=23% Similarity=0.562 Sum_probs=24.1
Q ss_pred ceeeeecCCcceeeecc-CCCceecccCCCCceeec
Q 017955 23 QYWCHHCEKRVSIETLA-NLPDVICHECKNGFVESI 57 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~-~~~~~~c~~C~~gFve~~ 57 (363)
.|.|-.|...|.+...- ....+.||.|++.=++.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 58999999766655321 124567999999656555
No 155
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.61 E-value=2.1 Score=45.32 Aligned_cols=46 Identities=37% Similarity=0.867 Sum_probs=38.1
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
....|.||+..+ ..+..+|. |..|+.+|+-.+..||+|+..+..++
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~ 523 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD 523 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence 456799999987 35666788 89999999999999999988776554
No 156
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.81 E-value=3.8 Score=28.80 Aligned_cols=29 Identities=28% Similarity=0.625 Sum_probs=21.7
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
.|-|-.|...|... ....+.||+|+.--+
T Consensus 2 ~Y~C~~Cg~~~~~~---~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK---SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC---CCCceECCCCCceEE
Confidence 48899999655544 356799999997544
No 157
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.88 E-value=2.4 Score=25.63 Aligned_cols=22 Identities=23% Similarity=0.703 Sum_probs=15.7
Q ss_pred eeeecCCcceeeeccCCCceecccCCCC
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
+|.+|. .++.... ..||+|+.-
T Consensus 1 ~Cp~CG----~~~~~~~--~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCG----AEIEDDA--KFCPNCGTP 22 (23)
T ss_pred CCcccC----CCCCCcC--cchhhhCCc
Confidence 588999 5555443 669999864
No 158
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=65.78 E-value=4 Score=37.72 Aligned_cols=42 Identities=26% Similarity=0.777 Sum_probs=28.2
Q ss_pred cccccccccc-----ccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955 280 ETIVCAICKD-----TVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326 (363)
Q Consensus 280 ~~~~C~ICle-----~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~ 326 (363)
.+..|-||-+ .|......+.-.|+-+||..|.. +..||-|-+
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 3567888875 23332344444599999999965 267999943
No 159
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=65.72 E-value=1.5 Score=40.86 Aligned_cols=71 Identities=21% Similarity=0.428 Sum_probs=47.6
Q ss_pred CCCCCCCceeeeecCCcceeeeccC--------CCceecccCCCCceeeccCCCCCCCCCCCCCCCCCCCCCc----hhh
Q 017955 16 ASDTDPTQYWCHHCEKRVSIETLAN--------LPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSF----GSQ 83 (363)
Q Consensus 16 ~~~~~~~~~~C~~C~~~~~~~~~~~--------~~~~~c~~C~~gFve~~~~~~~~~~~~~~~~~~~~~~~~~----~~~ 83 (363)
.+.++...|-|+.|.|.|..-...+ +--+.|-.|++||-.......+... - . +| -+.. .-.
T Consensus 110 gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt--h---t-gv-rpykc~~c~ka 182 (267)
T KOG3576|consen 110 GSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT--H---T-GV-RPYKCSLCEKA 182 (267)
T ss_pred cCCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcc--c---c-Cc-cccchhhhhHH
Confidence 4455689999999999998764333 3456799999999998877766441 0 1 12 1221 224
Q ss_pred hHHHHHHHHh
Q 017955 84 FLQVLRLIAQ 93 (363)
Q Consensus 84 ~~~~~~~~~~ 93 (363)
|+|++.|-++
T Consensus 183 ftqrcslesh 192 (267)
T KOG3576|consen 183 FTQRCSLESH 192 (267)
T ss_pred HHhhccHHHH
Confidence 8888877655
No 160
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.48 E-value=3.9 Score=39.89 Aligned_cols=38 Identities=13% Similarity=0.401 Sum_probs=28.6
Q ss_pred cccccccccccccCCceEEeC--CCCcccHhhHHHHHhcCC
Q 017955 281 TIVCAICKDTVNVGETATKLP--CGHVYHGDCIVPWLDSRN 319 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LP--C~H~Fh~~CI~~WLk~~~ 319 (363)
-+.|.+|.+-+.+-+ .+..| =.|+||..|-.+.+|...
T Consensus 268 pLcCTLC~ERLEDTH-FVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTH-FVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred ceeehhhhhhhccCc-eeecCCCcccceecccCHHHHHhhc
Confidence 378999999887543 33333 379999999999998743
No 161
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.51 E-value=2.8 Score=38.09 Aligned_cols=36 Identities=17% Similarity=0.496 Sum_probs=27.0
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
+..-|.|-.|.++++..-... -+++||.|++-.++-
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~-~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME-YGFRCPQCGEMLEEY 149 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh-cCCcCCCCCCCCeec
Confidence 456799999998777663222 479999999887763
No 162
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=63.50 E-value=5.6 Score=39.48 Aligned_cols=48 Identities=23% Similarity=0.454 Sum_probs=35.3
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~ 327 (363)
....|-.|......+...+.-.|+|+||.+|=.---..-..||-|-..
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~ 376 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEHK 376 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCCC
Confidence 344599997777766666666799999999965544555689999643
No 163
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=63.42 E-value=3.1 Score=31.45 Aligned_cols=29 Identities=21% Similarity=0.472 Sum_probs=18.8
Q ss_pred eeeecCCcceeeeccCCCceecccCCCC-ceeeccC
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNG-FVESIPV 59 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~g-Fve~~~~ 59 (363)
-|++|.+-+... .-+||.|++- |.|+-..
T Consensus 6 AC~~Ck~l~~~d------~e~CP~Cgs~~~te~W~G 35 (64)
T COG2093 6 ACKNCKRLTPED------TEICPVCGSTDLTEEWFG 35 (64)
T ss_pred HHhhccccCCCC------CccCCCCCCcccchhhcc
Confidence 389998322221 2469999998 8777543
No 164
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=63.40 E-value=4 Score=28.17 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=14.6
Q ss_pred ceeeeccCCCceecccCCCCce
Q 017955 33 VSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 33 ~~~~~~~~~~~~~c~~C~~gFv 54 (363)
|.+.+...-.-++||||+.-||
T Consensus 19 Vyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 19 VYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp EEEE-TTTTCEEEETTTTEEEE
T ss_pred EEEecCCCCCeEECCCCCCEEC
Confidence 4455554433599999998776
No 165
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.37 E-value=7.1 Score=32.25 Aligned_cols=38 Identities=21% Similarity=0.490 Sum_probs=31.9
Q ss_pred CCceeeeecC-CcceeeeccCCCceecccCCCCceeecc
Q 017955 21 PTQYWCHHCE-KRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 21 ~~~~~C~~C~-~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
+.-|-|-.|. ..|++.+....+.++|+.|+-.|-..|+
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~ 57 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVP 57 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECC
Confidence 4589999999 6666677777899999999999888765
No 166
>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=63.15 E-value=2.6 Score=28.35 Aligned_cols=33 Identities=21% Similarity=0.495 Sum_probs=26.6
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCcee
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
|..|-.|.+..-+...|...+.+|..|++.+|+
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 467889998888889999999999999997775
No 167
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=62.50 E-value=4.9 Score=28.34 Aligned_cols=32 Identities=19% Similarity=0.556 Sum_probs=20.7
Q ss_pred eeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
||-.|...+.......-.-++||.|+ |+..++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 79999865544433222368999998 555554
No 168
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=62.01 E-value=4.5 Score=36.81 Aligned_cols=27 Identities=22% Similarity=0.596 Sum_probs=20.9
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
..+|-||-|.+-|. .|--+||.|++--
T Consensus 137 ~w~~rC~GC~~~f~------~~~~~Cp~CG~~~ 163 (177)
T COG1439 137 KWRLRCHGCKRIFP------EPKDFCPICGSPL 163 (177)
T ss_pred eeeEEEecCceecC------CCCCcCCCCCCce
Confidence 45788999995555 5557899999983
No 169
>PF14968 CCDC84: Coiled coil protein 84
Probab=61.80 E-value=4.2 Score=40.66 Aligned_cols=34 Identities=21% Similarity=0.656 Sum_probs=25.8
Q ss_pred CCCCceeeeecCCcceeeeccCCCceecccCCCCceeeccCC
Q 017955 19 TDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVT 60 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~ 60 (363)
....+||||.|. .+|.....-+.| +|.|+-|..+
T Consensus 54 ~~~~~fWC~fC~----~ev~~~~s~~~~----~~ai~HLaS~ 87 (336)
T PF14968_consen 54 EHRNRFWCVFCD----CEVREHDSSFAC----GGAIEHLASP 87 (336)
T ss_pred cccceeEeeCcc----chhhhccchhhh----ccHHhhcCCH
Confidence 568899999999 777777665555 6788877643
No 170
>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=61.74 E-value=2.7 Score=37.43 Aligned_cols=35 Identities=11% Similarity=0.265 Sum_probs=25.7
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCcee
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
...-|.|-.|.++++..-... -+++||.|++-.++
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~-~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME-LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH-cCCcCCCCCCEeee
Confidence 456789999998777663333 37999999986544
No 171
>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=61.72 E-value=7.2 Score=25.04 Aligned_cols=38 Identities=32% Similarity=0.674 Sum_probs=24.9
Q ss_pred cccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
.|..|...+....... ..=+..||..|. .|..|+..|.
T Consensus 1 ~C~~C~~~i~~~~~~~-~~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVL-RALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEE-EeCCccccccCC--------CCcccCCcCc
Confidence 3788888776542222 223678888885 6888887764
No 172
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=61.51 E-value=7 Score=42.89 Aligned_cols=12 Identities=33% Similarity=0.551 Sum_probs=5.3
Q ss_pred hhhHHHHhhhhc
Q 017955 175 EDEEDLRRRWRD 186 (363)
Q Consensus 175 ~~e~~~rr~~r~ 186 (363)
..+.++.+.+|+
T Consensus 931 kdwdele~ea~~ 942 (960)
T KOG1189|consen 931 KDWDELEREARN 942 (960)
T ss_pred cchhhhHHHHhh
Confidence 334444444443
No 173
>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=61.35 E-value=4.8 Score=30.80 Aligned_cols=13 Identities=15% Similarity=0.731 Sum_probs=9.3
Q ss_pred cccHhhHHHHHhc
Q 017955 305 VYHGDCIVPWLDS 317 (363)
Q Consensus 305 ~Fh~~CI~~WLk~ 317 (363)
-||+.||.+|++.
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999863
No 174
>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=60.76 E-value=6.6 Score=25.74 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=17.7
Q ss_pred eeeeecCCcceeeeccCCCceecccCCCC
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
|-|-.|.+.|..+ ....+.|++|+.-
T Consensus 1 Y~C~~Cg~~~~~~---~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK---PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS---TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC---CCCcEECCcCCCe
Confidence 6799999777633 3345799999853
No 175
>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=59.45 E-value=6.3 Score=34.01 Aligned_cols=34 Identities=12% Similarity=0.050 Sum_probs=26.0
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
+.++-|..|.++|- .++-.-++||+|+.-|..+.
T Consensus 7 GtKr~Cp~cg~kFY---DLnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 7 GTKRICPNTGSKFY---DLNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred CccccCCCcCcccc---ccCCCCccCCCcCCccCcch
Confidence 45788999996664 44456689999999986663
No 176
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=59.13 E-value=7.7 Score=38.42 Aligned_cols=46 Identities=22% Similarity=0.540 Sum_probs=36.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC---CCCCcC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCR 325 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~---sCPlCR 325 (363)
.-..|||-.+.-.....+..|.|+|+.-..-+....++.. .||.|-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 3457998777666666888999999999999988777644 799994
No 177
>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 KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=58.09 E-value=10 Score=28.33 Aligned_cols=38 Identities=29% Similarity=0.561 Sum_probs=25.5
Q ss_pred CCCCCCCCCCC--CCCceeeeecCCcceeeeccCCCc-eecccCC
Q 017955 9 PTPTTPTASDT--DPTQYWCHHCEKRVSIETLANLPD-VICHECK 50 (363)
Q Consensus 9 ~~~~~~~~~~~--~~~~~~C~~C~~~~~~~~~~~~~~-~~c~~C~ 50 (363)
+|.+.++|+.. ++-.|-|-.|. .+-..+.-| +-|-.|+
T Consensus 4 ~~s~~~~aa~~r~~~miYiCgdC~----~en~lk~~D~irCReCG 44 (62)
T KOG3507|consen 4 PTSLGDPAAGPRTATMIYICGDCG----QENTLKRGDVIRCRECG 44 (62)
T ss_pred ccCCCCccCCCCcccEEEEecccc----ccccccCCCcEehhhcc
Confidence 34445555444 78899999999 775555544 4588886
No 179
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.07 E-value=5.8 Score=26.50 Aligned_cols=30 Identities=23% Similarity=0.566 Sum_probs=22.7
Q ss_pred eeeeecCCcceee---eccCCCceecccCCCCc
Q 017955 24 YWCHHCEKRVSIE---TLANLPDVICHECKNGF 53 (363)
Q Consensus 24 ~~C~~C~~~~~~~---~~~~~~~~~c~~C~~gF 53 (363)
.-|.+|.+.+.+. |.+..-.+.|+.|+.-|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4588999887776 44556679999998765
No 180
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.80 E-value=6.4 Score=37.71 Aligned_cols=32 Identities=13% Similarity=0.352 Sum_probs=27.8
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD 316 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk 316 (363)
..|..||..+. .+++.|=||+|++.||.+++-
T Consensus 44 dcCsLtLqPc~---dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 44 DCCSLTLQPCR---DPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ceeeeeccccc---CCccCCCCeeeeHHHHHHHHH
Confidence 56999999887 678888999999999999863
No 181
>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=57.73 E-value=5.2 Score=24.96 Aligned_cols=23 Identities=26% Similarity=0.681 Sum_probs=16.4
Q ss_pred eeecCCcceeeeccCCCceecccCCCCce
Q 017955 26 CHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
|-.|.+.|+. ...+||.|+--|.
T Consensus 3 CP~C~~~V~~------~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPE------SAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchh------hcCcCCCCCCCCc
Confidence 7788855533 3357999998885
No 182
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=57.40 E-value=4.8 Score=27.43 Aligned_cols=30 Identities=17% Similarity=0.525 Sum_probs=22.3
Q ss_pred eeecCCcceeeeccCCCceecccCCCCcee
Q 017955 26 CHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
|-+|...........++-.+|+.|++-|+.
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 777876555555566777889999998874
No 183
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.19 E-value=5.1 Score=35.08 Aligned_cols=40 Identities=23% Similarity=0.492 Sum_probs=27.9
Q ss_pred CCCCceeeeecCCcceeeeccCC--Cc--eecccCCCCceeecc
Q 017955 19 TDPTQYWCHHCEKRVSIETLANL--PD--VICHECKNGFVESIP 58 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~~~~~--~~--~~c~~C~~gFve~~~ 58 (363)
....-|.|-+|.+.++..-...+ ++ ++||.|+.-.++.-+
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 34668999999988876422221 23 999999987776544
No 184
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.84 E-value=5.5 Score=43.75 Aligned_cols=46 Identities=22% Similarity=0.512 Sum_probs=33.5
Q ss_pred ccccccccccccc-C---CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcC
Q 017955 281 TIVCAICKDTVNV-G---ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327 (363)
Q Consensus 281 ~~~C~ICle~f~~-~---e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~ 327 (363)
...|.-|+..... + ..++.+-|+|+||..|+.--..+++ |-.|-..
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~~ 833 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESGK 833 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhce
Confidence 3579999886552 2 3677888999999999988765555 6666443
No 185
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=56.48 E-value=5.9 Score=38.29 Aligned_cols=48 Identities=23% Similarity=0.571 Sum_probs=33.0
Q ss_pred ccccccccccc-cCCceEEeC---CCCcccHhhHHHHHhc---------CCCCCCcCcCCC
Q 017955 282 IVCAICKDTVN-VGETATKLP---CGHVYHGDCIVPWLDS---------RNTCPVCRFELP 329 (363)
Q Consensus 282 ~~C~ICle~f~-~~e~~~~LP---C~H~Fh~~CI~~WLk~---------~~sCPlCR~~l~ 329 (363)
..|-||...+. .+..+...| |.-++|..|+-.-+.. ...||.|++.+.
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 47999999884 322222222 8889999999995543 237999998554
No 186
>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=55.35 E-value=5.4 Score=28.76 Aligned_cols=10 Identities=40% Similarity=1.066 Sum_probs=4.8
Q ss_pred eecccCCCCc
Q 017955 44 VICHECKNGF 53 (363)
Q Consensus 44 ~~c~~C~~gF 53 (363)
|.||+|+.+|
T Consensus 3 f~CP~C~~~~ 12 (54)
T PF05605_consen 3 FTCPYCGKGF 12 (54)
T ss_pred cCCCCCCCcc
Confidence 4455555443
No 187
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=55.16 E-value=12 Score=35.48 Aligned_cols=11 Identities=9% Similarity=0.244 Sum_probs=6.3
Q ss_pred HHHHHHHHhhh
Q 017955 85 LQVLRLIAQAA 95 (363)
Q Consensus 85 ~~~~~~~~~~~ 95 (363)
..|-.||.+..
T Consensus 12 nrm~~LL~~E~ 22 (240)
T PF05764_consen 12 NRMKKLLEEEL 22 (240)
T ss_pred HHHHHHHHHHH
Confidence 45556666654
No 188
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=54.91 E-value=8.7 Score=33.93 Aligned_cols=32 Identities=22% Similarity=0.568 Sum_probs=24.9
Q ss_pred CCCCceeeeecCCcceeeeccCCCceecccCCCC
Q 017955 19 TDPTQYWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
..+++|-|-+|...+.......+ -.||.|++.
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~~~~l--~~Cp~C~~~ 139 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTHPERL--PPCPKCGHT 139 (146)
T ss_pred ecCceEecccCCCEEEecCCCcC--CCCCCCCCC
Confidence 45789999999977777755555 359999975
No 189
>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=54.66 E-value=8.7 Score=27.94 Aligned_cols=41 Identities=27% Similarity=0.624 Sum_probs=20.0
Q ss_pred ccccccccccCC------ceEEeC-CCCcccHhhHHHHHhcCCCCCCc
Q 017955 284 CAICKDTVNVGE------TATKLP-CGHVYHGDCIVPWLDSRNTCPVC 324 (363)
Q Consensus 284 C~ICle~f~~~e------~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlC 324 (363)
|--|+..|.... ....-| |++.||.+|=.---..-..||-|
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC 49 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGC 49 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCC
Confidence 445666665431 234445 99999999943322344579988
No 190
>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=54.54 E-value=6.2 Score=27.65 Aligned_cols=43 Identities=28% Similarity=0.697 Sum_probs=29.4
Q ss_pred cccccccccccCCceEEeCCCCcccHhhHHHHHhc------CCCCCCcC
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS------RNTCPVCR 325 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~------~~sCPlCR 325 (363)
.|.||......+..+..-.|...||..|+..=.+. .-.||.|+
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 48899985554445555569999999998765431 22677774
No 191
>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=54.34 E-value=6.1 Score=25.18 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=17.7
Q ss_pred eeeeecCCcceeeeccCCCceecccCC
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
|||.-|. .++.... -|.|..|.
T Consensus 1 ~~C~~C~----~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCR----RKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCCC----CCcCCCE-eEEeCCCC
Confidence 7999999 6666664 69999987
No 192
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=52.93 E-value=12 Score=37.04 Aligned_cols=52 Identities=27% Similarity=0.630 Sum_probs=34.5
Q ss_pred ccccccccccccc-----cCC-----------ceEEeCCCCcccHhhHHHHHhc---------CCCCCCcCcCCCCC
Q 017955 280 ETIVCAICKDTVN-----VGE-----------TATKLPCGHVYHGDCIVPWLDS---------RNTCPVCRFELPTD 331 (363)
Q Consensus 280 ~~~~C~ICle~f~-----~~e-----------~~~~LPC~H~Fh~~CI~~WLk~---------~~sCPlCR~~l~~~ 331 (363)
....||||+..-. .+- .-.--||+|+--..-.+-|.+. +..||.|-..|...
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 3578999987421 000 0112379998888888888775 34799998877554
No 193
>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=52.49 E-value=11 Score=24.52 Aligned_cols=26 Identities=19% Similarity=0.414 Sum_probs=19.1
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
+|-|-.|. -...+..++..||.|+.+
T Consensus 1 ~~~C~~CG----y~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCG----YIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCC----CEECCCcCCCcCcCCCCc
Confidence 46788888 444566688899999864
No 194
>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=52.24 E-value=9 Score=23.55 Aligned_cols=22 Identities=18% Similarity=0.456 Sum_probs=14.7
Q ss_pred eeecCCcceeeeccC--CCceecccCCC
Q 017955 26 CHHCEKRVSIETLAN--LPDVICHECKN 51 (363)
Q Consensus 26 C~~C~~~~~~~~~~~--~~~~~c~~C~~ 51 (363)
|..|. ..|.+. .-.|.||.|+.
T Consensus 1 C~sC~----~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCG----RPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCC----CcccCcccCceEeCCCCCC
Confidence 67787 444444 35688999973
No 195
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=51.18 E-value=6.9 Score=26.38 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=7.8
Q ss_pred eecccCCCCce
Q 017955 44 VICHECKNGFV 54 (363)
Q Consensus 44 ~~c~~C~~gFv 54 (363)
-.||+|++||-
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 196
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=50.68 E-value=15 Score=39.80 Aligned_cols=9 Identities=11% Similarity=0.047 Sum_probs=3.8
Q ss_pred HHHHHHhhh
Q 017955 87 VLRLIAQAA 95 (363)
Q Consensus 87 ~~~~~~~~~ 95 (363)
.|.-|-.+.
T Consensus 899 nW~timksi 907 (1001)
T COG5406 899 NWNTIMKSI 907 (1001)
T ss_pred cHHHHHHHH
Confidence 344444433
No 197
>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=50.66 E-value=5.2 Score=23.24 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=9.2
Q ss_pred eecccCCCCcee
Q 017955 44 VICHECKNGFVE 55 (363)
Q Consensus 44 ~~c~~C~~gFve 55 (363)
++|+.|+..|..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 578899888853
No 198
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=49.85 E-value=9.8 Score=32.95 Aligned_cols=35 Identities=17% Similarity=0.410 Sum_probs=25.6
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCcee
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
.-.|.|-.|...+......+...+.|+.|++-|+.
T Consensus 121 ~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred ceEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 45677888997766654446678999999976653
No 199
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=49.41 E-value=8.2 Score=24.38 Aligned_cols=27 Identities=15% Similarity=0.455 Sum_probs=14.6
Q ss_pred eeeecCCcceeeeccCCCceecccCCC
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
-|.+|...+.......-..++||+|..
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 377777666555555556678888853
No 200
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=48.52 E-value=14 Score=26.71 Aligned_cols=42 Identities=21% Similarity=0.513 Sum_probs=29.2
Q ss_pred CCceeee--ecCCcceeeeccCCCceecccCCCCceeeccCCCC
Q 017955 21 PTQYWCH--HCEKRVSIETLANLPDVICHECKNGFVESIPVTLT 62 (363)
Q Consensus 21 ~~~~~C~--~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~~~ 62 (363)
...-||. .|...+...-....+.++||.|+--|--.=....|
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 4566999 99866555434467889999999888654444433
No 201
>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=48.38 E-value=9.8 Score=28.47 Aligned_cols=37 Identities=22% Similarity=0.466 Sum_probs=18.3
Q ss_pred cccccccccccccccCCceEEe-CCCCcccHhhHHHHH
Q 017955 279 QETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWL 315 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WL 315 (363)
.....|.+|...|..-..-..- .||++||..|....+
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 3557899999999743222222 399999999986543
No 202
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.16 E-value=3.6 Score=39.74 Aligned_cols=47 Identities=26% Similarity=0.567 Sum_probs=38.1
Q ss_pred cccccccccccccC---CceEEeC--------CCCcccHhhHHHHHhcCC-CCCCcCcC
Q 017955 281 TIVCAICKDTVNVG---ETATKLP--------CGHVYHGDCIVPWLDSRN-TCPVCRFE 327 (363)
Q Consensus 281 ~~~C~ICle~f~~~---e~~~~LP--------C~H~Fh~~CI~~WLk~~~-sCPlCR~~ 327 (363)
...|.||...|... ..+..+. |+|..|..|+..-+.+.. .||.||+.
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 46699999988732 2566677 999999999999987765 89999874
No 203
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.90 E-value=6.5 Score=38.66 Aligned_cols=47 Identities=26% Similarity=0.586 Sum_probs=37.8
Q ss_pred ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
....|.||...+. .+.+.. |.|.|+..|...|....+-||.||....
T Consensus 104 ~~~~~~~~~g~l~---vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~ 151 (324)
T KOG0824|consen 104 DHDICYICYGKLT---VPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGKIS 151 (324)
T ss_pred CccceeeeeeeEE---ecccccCceeeeeecCCchhhhhhhccchhhcCcC
Confidence 3467999998877 334443 9999999999999999999999987554
No 204
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=47.80 E-value=14 Score=37.53 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=12.4
Q ss_pred CChhhHHHHHcCCceeeec
Q 017955 259 APRAAKSAVLELPTVEILS 277 (363)
Q Consensus 259 ~~~~s~~~i~~lp~~~~~~ 277 (363)
..++...-|.+||.+++..
T Consensus 413 ~Lp~eEQMIsALPDiK~l~ 431 (542)
T KOG0699|consen 413 ELPLEEQMISALPDIKILA 431 (542)
T ss_pred CCChHHHHhhhcccceeEe
Confidence 3445566778888777654
No 205
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=47.40 E-value=6.2 Score=43.33 Aligned_cols=9 Identities=22% Similarity=-0.020 Sum_probs=0.0
Q ss_pred CCCcCcCCC
Q 017955 321 CPVCRFELP 329 (363)
Q Consensus 321 CPlCR~~l~ 329 (363)
+|..-..+.
T Consensus 651 lPs~~~~~~ 659 (713)
T PF03344_consen 651 LPSPMDPLT 659 (713)
T ss_dssp ---------
T ss_pred ccccccccc
Confidence 444444433
No 206
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.01 E-value=18 Score=30.64 Aligned_cols=44 Identities=25% Similarity=0.408 Sum_probs=32.8
Q ss_pred ccccccccccccCC----------ceE-EeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955 282 IVCAICKDTVNVGE----------TAT-KLPCGHVYHGDCIVPWLDSRNTCPVCR 325 (363)
Q Consensus 282 ~~C~ICle~f~~~e----------~~~-~LPC~H~Fh~~CI~~WLk~~~sCPlCR 325 (363)
..|--|+..|.... ... ...|++.||.+|=.-|-..-..||-|-
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 45999999886321 112 234999999999888888878899995
No 207
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=46.88 E-value=9.8 Score=25.82 Aligned_cols=20 Identities=20% Similarity=0.835 Sum_probs=16.5
Q ss_pred eeccCCCceecccCCCCcee
Q 017955 36 ETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 36 ~~~~~~~~~~c~~C~~gFve 55 (363)
-+..++|-.+|+.|+..|+.
T Consensus 25 ~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 25 IVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred EEEeCCCccccccCCCEeeC
Confidence 35667899999999999874
No 208
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=46.70 E-value=12 Score=24.99 Aligned_cols=30 Identities=27% Similarity=0.540 Sum_probs=21.2
Q ss_pred eeeecCCcceeeec---cCCCceecccCCCCce
Q 017955 25 WCHHCEKRVSIETL---ANLPDVICHECKNGFV 54 (363)
Q Consensus 25 ~C~~C~~~~~~~~~---~~~~~~~c~~C~~gFv 54 (363)
-|.+|...+.+.-. ..--.+.|+.|+.-|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 48888877766533 4456789999987763
No 209
>PRK12496 hypothetical protein; Provisional
Probab=46.68 E-value=11 Score=33.85 Aligned_cols=27 Identities=22% Similarity=0.603 Sum_probs=20.0
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
+|.|.-|. .....+.+.-+||.||+--
T Consensus 127 ~~~C~gC~----~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCK----KKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCC----ccccCCCCCCcCCCCCChh
Confidence 58899999 5555555556899999753
No 210
>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=46.52 E-value=6.6 Score=39.99 Aligned_cols=32 Identities=38% Similarity=0.648 Sum_probs=0.0
Q ss_pred ceEEeCCCCcccHhhHHHHHhc------CCCCCCcCcCCCC
Q 017955 296 TATKLPCGHVYHGDCIVPWLDS------RNTCPVCRFELPT 330 (363)
Q Consensus 296 ~~~~LPC~H~Fh~~CI~~WLk~------~~sCPlCR~~l~~ 330 (363)
.-+-|.|||++.+ ..|-.. ..+||+||..=+.
T Consensus 303 P~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g~~ 340 (416)
T PF04710_consen 303 PWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVGPY 340 (416)
T ss_dssp -----------------------------------------
T ss_pred ceeeccccceeee---cccccccccccccccCCCccccCCc
Confidence 3455679998874 568542 3479999985443
No 211
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=46.40 E-value=20 Score=38.96 Aligned_cols=55 Identities=20% Similarity=0.384 Sum_probs=33.6
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CC-----CCCCcCcCCCCCChhHHHH
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RN-----TCPVCRFELPTDDPEYEEE 338 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~-----sCPlCR~~l~~~d~~~~~~ 338 (363)
-.+.|+|+.-.+.. .++.+.|+|+=|.+-. |+-+ +. .||+|.+....++...+..
T Consensus 305 vSL~CPl~~~Rm~~--P~r~~~CkHlQcFD~~--~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~ 365 (636)
T KOG2169|consen 305 VSLNCPLSKMRMSL--PARGHTCKHLQCFDAL--SYLQMNEQKPTWRCPVCQKAAPFEGLIIDGY 365 (636)
T ss_pred eEecCCcccceeec--CCcccccccceecchh--hhHHhccCCCeeeCccCCccccccchhhhHH
Confidence 34779998876542 3334446665555442 4322 11 6999999888887665544
No 212
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=45.41 E-value=7 Score=31.16 Aligned_cols=6 Identities=33% Similarity=0.706 Sum_probs=0.7
Q ss_pred HHHHhh
Q 017955 209 WAEILN 214 (363)
Q Consensus 209 ~~~il~ 214 (363)
|-.||-
T Consensus 67 wlwLli 72 (81)
T PF14812_consen 67 WLWLLI 72 (81)
T ss_dssp ----TT
T ss_pred hHHHHH
Confidence 333333
No 213
>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=45.19 E-value=7.2 Score=23.90 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=8.7
Q ss_pred eecccCCCCce
Q 017955 44 VICHECKNGFV 54 (363)
Q Consensus 44 ~~c~~C~~gFv 54 (363)
+.|+.|+..|.
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 78888888774
No 214
>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=45.17 E-value=12 Score=27.49 Aligned_cols=32 Identities=28% Similarity=0.556 Sum_probs=23.7
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
.|-|-.|...+.+.-...-.-+.||.|+.-|-
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 47799999777665444456789999998763
No 215
>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=44.16 E-value=7.5 Score=39.58 Aligned_cols=50 Identities=28% Similarity=0.619 Sum_probs=0.0
Q ss_pred ccccccccccccc-----CC-----------ceEEeCCCCcccHhhHHHHHhc---------CCCCCCcCcCCCC
Q 017955 281 TIVCAICKDTVNV-----GE-----------TATKLPCGHVYHGDCIVPWLDS---------RNTCPVCRFELPT 330 (363)
Q Consensus 281 ~~~C~ICle~f~~-----~e-----------~~~~LPC~H~Fh~~CI~~WLk~---------~~sCPlCR~~l~~ 330 (363)
...|+||+..-.. |. .-.--||||+--....+-|.+. +..||.|-..|..
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 5689999864220 10 1223389999988899999764 2479999888764
No 216
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=43.15 E-value=14 Score=36.31 Aligned_cols=29 Identities=21% Similarity=0.513 Sum_probs=23.3
Q ss_pred eeeecCCcce-eeeccCCCceecccCCCCc
Q 017955 25 WCHHCEKRVS-IETLANLPDVICHECKNGF 53 (363)
Q Consensus 25 ~C~~C~~~~~-~~~~~~~~~~~c~~C~~gF 53 (363)
||+.|.++-. +-++....|.+|+.|+=-|
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeee
Confidence 8999997766 5566777999999998654
No 217
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=42.98 E-value=20 Score=37.49 Aligned_cols=36 Identities=22% Similarity=0.521 Sum_probs=26.0
Q ss_pred CCCCCCCCCCceeeeecCCcceeeecc----------------CCC-ceecccCCCC
Q 017955 13 TPTASDTDPTQYWCHHCEKRVSIETLA----------------NLP-DVICHECKNG 52 (363)
Q Consensus 13 ~~~~~~~~~~~~~C~~C~~~~~~~~~~----------------~~~-~~~c~~C~~g 52 (363)
+-+|......+|-|-.|. -.-+| +|| +.+||.|+.+
T Consensus 415 ~~~~~~~~~~~~~c~~c~----~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 415 SATTTADLGPRMQCSVCQ----WIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred ccccccCCCCeEEECCCC----eEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 345556678899999999 44333 354 7899999865
No 218
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=42.86 E-value=15 Score=40.47 Aligned_cols=6 Identities=50% Similarity=0.789 Sum_probs=2.3
Q ss_pred hHHHHH
Q 017955 241 GYEALL 246 (363)
Q Consensus 241 ~~e~Ll 246 (363)
.|..|+
T Consensus 971 ey~hll 976 (988)
T KOG2038|consen 971 EYAHLL 976 (988)
T ss_pred HHHHHh
Confidence 333333
No 219
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=42.73 E-value=26 Score=27.77 Aligned_cols=49 Identities=24% Similarity=0.543 Sum_probs=20.8
Q ss_pred cccccccccccccc---CCc-eEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCC
Q 017955 280 ETIVCAICKDTVNV---GET-ATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~---~e~-~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l 328 (363)
....|.||-+.+.. ++. +....|+--.|+.|..-=.+. ++.||.|+...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 34679999987763 222 333348888999998765554 56899998655
No 220
>PHA00616 hypothetical protein
Probab=42.04 E-value=6.4 Score=27.77 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=10.7
Q ss_pred eecccCCCCceee
Q 017955 44 VICHECKNGFVES 56 (363)
Q Consensus 44 ~~c~~C~~gFve~ 56 (363)
+.|++|++.|+..
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 5699999999754
No 221
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.60 E-value=16 Score=40.43 Aligned_cols=31 Identities=26% Similarity=0.640 Sum_probs=20.8
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
..+...||+|..+ +..| ..||.|++--+.-.
T Consensus 459 ~~~~L~CH~Cg~~---~~~p----~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 459 ATGQLRCHYCGYQ---EPIP----QSCPECGSEHLRAV 489 (730)
T ss_pred CCCeeEeCCCCCC---CCCC----CCCCCCCCCeeEEe
Confidence 3578899999933 2222 34999998755443
No 222
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=40.37 E-value=15 Score=36.49 Aligned_cols=26 Identities=15% Similarity=0.498 Sum_probs=18.8
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
...-+||-|. +.-. .|+||+|+--+-
T Consensus 5 s~~~~C~ic~----vq~~----~YtCPRCn~~YC 30 (383)
T KOG4317|consen 5 SSFLACGICG----VQKR----EYTCPRCNLLYC 30 (383)
T ss_pred Cceeeccccc----cccc----cccCCCCCccce
Confidence 3478999999 4322 399999986554
No 223
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=40.10 E-value=24 Score=33.91 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=23.8
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCC
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
...|+-|-||...|.--....-.-..||+|++
T Consensus 154 ~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrK 185 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFNTLTSNTLARCPHCRK 185 (256)
T ss_pred CceeEECCCCCCcEeccCCCCCccccCCCCce
Confidence 46789999999777665544334579999985
No 224
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=39.93 E-value=24 Score=29.34 Aligned_cols=24 Identities=25% Similarity=0.580 Sum_probs=19.0
Q ss_pred CCcccHhhHHHHHhc---------CCCCCCcCc
Q 017955 303 GHVYHGDCIVPWLDS---------RNTCPVCRF 326 (363)
Q Consensus 303 ~H~Fh~~CI~~WLk~---------~~sCPlCR~ 326 (363)
.-.||..||..++.. .-.||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 678999999998753 226999987
No 225
>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=39.79 E-value=17 Score=37.34 Aligned_cols=29 Identities=17% Similarity=0.581 Sum_probs=21.9
Q ss_pred eeeecCCcceeeeccCCCceecccCCCCc
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
-||+|..-+.+.-.+.-....||+|+.--
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 49999976666655556678899999754
No 226
>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=39.14 E-value=3.5 Score=40.09 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=20.9
Q ss_pred ccccccccccccccCCceEEe--CCCCcccHhhHHHHHhcCCCCCCcCcC
Q 017955 280 ETIVCAICKDTVNVGETATKL--PCGHVYHGDCIVPWLDSRNTCPVCRFE 327 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~L--PC~H~Fh~~CI~~WLk~~~sCPlCR~~ 327 (363)
....||||-..-........- -=.|.+|.-|-..|--.+..||.|-..
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 346899997643311100000 024678888999998888899999654
No 227
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=38.82 E-value=15 Score=37.86 Aligned_cols=29 Identities=28% Similarity=0.569 Sum_probs=19.7
Q ss_pred eecCCcceeeeccCCCceecccCCCCceeeccCCCC
Q 017955 27 HHCEKRVSIETLANLPDVICHECKNGFVESIPVTLT 62 (363)
Q Consensus 27 ~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~~~ 62 (363)
|+|.+-|.+| |.||+|++-|-==-+..+|
T Consensus 286 HrC~RIV~vE-------YrCPEC~KVFsCPANLASH 314 (500)
T KOG3993|consen 286 HRCPRIVHVE-------YRCPECDKVFSCPANLASH 314 (500)
T ss_pred ccCCeeEEee-------ecCCcccccccCchhhhhh
Confidence 6777555554 7899999999554444444
No 228
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=38.70 E-value=36 Score=33.01 Aligned_cols=56 Identities=27% Similarity=0.465 Sum_probs=32.7
Q ss_pred cccccccccccccCCceEEeC-CC-CcccHhhHHHHH-hcCCCCCCcCcCCCCCChhHHHHHH
Q 017955 281 TIVCAICKDTVNVGETATKLP-CG-HVYHGDCIVPWL-DSRNTCPVCRFELPTDDPEYEEERK 340 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LP-C~-H~Fh~~CI~~WL-k~~~sCPlCR~~l~~~d~~~~~~~~ 340 (363)
-..|.||++....|-...-|. -+ =.=|++|..+|- .-+..|| |..+. -..|++++.
T Consensus 30 LsfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p--rsk~s--kStYe~vK~ 88 (285)
T PF06937_consen 30 LSFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP--RSKLS--KSTYEEVKT 88 (285)
T ss_pred eeecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCC--ccccc--cchHHHHHH
Confidence 356999988765443222222 11 145799999995 5566899 33332 233666654
No 229
>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=38.61 E-value=11 Score=27.14 Aligned_cols=30 Identities=33% Similarity=0.784 Sum_probs=16.4
Q ss_pred eeeee--cCCcceeeeccCCCceecccCCCCc
Q 017955 24 YWCHH--CEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 24 ~~C~~--C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
-||-. |...+........+.++|+.|+.-|
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 49988 9966666655555559999998766
No 230
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=37.83 E-value=18 Score=32.07 Aligned_cols=19 Identities=32% Similarity=0.877 Sum_probs=15.3
Q ss_pred CCCCCCCceeeeecCCcceee
Q 017955 16 ASDTDPTQYWCHHCEKRVSIE 36 (363)
Q Consensus 16 ~~~~~~~~~~C~~C~~~~~~~ 36 (363)
.+.++++||||-.|- |+..
T Consensus 119 ~a~vSPRRYFClQCH--VPQa 137 (155)
T COG3043 119 LADVSPRRYFCLQCH--VPQA 137 (155)
T ss_pred ccccCccceeeeecc--cccc
Confidence 567899999999998 4444
No 231
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=37.67 E-value=18 Score=37.28 Aligned_cols=30 Identities=20% Similarity=0.561 Sum_probs=22.4
Q ss_pred eeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
--||+|..-+.+.-.+.-.-..||+|+.--
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 449999977666655556678899999753
No 232
>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=37.66 E-value=14 Score=20.92 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=6.3
Q ss_pred eecccCCCCce
Q 017955 44 VICHECKNGFV 54 (363)
Q Consensus 44 ~~c~~C~~gFv 54 (363)
++|+.|+..|-
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 57888887664
No 233
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=37.36 E-value=7.6 Score=38.06 Aligned_cols=40 Identities=28% Similarity=0.631 Sum_probs=31.4
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN 319 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~ 319 (363)
....|.||++.|..+.....+-|..+||..|+..|++...
T Consensus 213 ~~rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (288)
T KOG1729|consen 213 PIRVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTGA 252 (288)
T ss_pred CceecHHHHHHHhcccccchhhcccccccccccccccccc
Confidence 3458999999998655566666766999999999998654
No 234
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=37.33 E-value=19 Score=35.76 Aligned_cols=11 Identities=9% Similarity=-0.052 Sum_probs=5.0
Q ss_pred hHHHHHHHHhh
Q 017955 84 FLQVLRLIAQA 94 (363)
Q Consensus 84 ~~~~~~~~~~~ 94 (363)
+....+|+.+.
T Consensus 67 ~i~G~elL~~~ 77 (324)
T PF05285_consen 67 GIPGAELLEEW 77 (324)
T ss_pred CCChHHHHHHH
Confidence 34444444443
No 235
>PRK13794 hypothetical protein; Provisional
Probab=37.12 E-value=16 Score=38.23 Aligned_cols=23 Identities=26% Similarity=0.869 Sum_probs=17.9
Q ss_pred CceeeeecCCcceeeeccCCCceecccCCCC
Q 017955 22 TQYWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 22 ~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
+=|||-.|+ +-+..+. |..|++.
T Consensus 9 ~~~wc~~cn----~p~~~~~----c~~cg~~ 31 (479)
T PRK13794 9 HLKWCDNCN----VPVLGKK----CAICGSE 31 (479)
T ss_pred EEEEcCCCC----CeecCCc----hhHhCCC
Confidence 469999999 5555444 9999995
No 236
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=36.86 E-value=19 Score=40.68 Aligned_cols=7 Identities=29% Similarity=0.719 Sum_probs=3.0
Q ss_pred hHHHHHH
Q 017955 241 GYEALLQ 247 (363)
Q Consensus 241 ~~e~Ll~ 247 (363)
.|+.|++
T Consensus 978 ~yq~l~~ 984 (1010)
T KOG1991|consen 978 RYQKLIS 984 (1010)
T ss_pred HHHHHHh
Confidence 3444443
No 237
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=36.29 E-value=22 Score=42.60 Aligned_cols=22 Identities=18% Similarity=0.170 Sum_probs=12.3
Q ss_pred eccCCCceecccCCCCceeecc
Q 017955 37 TLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 37 ~~~~~~~~~c~~C~~gFve~~~ 58 (363)
++-+.---+||.=+.|=-=||.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~ 108 (2849)
T PTZ00415 87 TSVKIKQRTCPFHKEGSSFEMG 108 (2849)
T ss_pred cccceecccCcccccccccccc
Confidence 3344455668877666544443
No 238
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=35.84 E-value=32 Score=39.47 Aligned_cols=49 Identities=27% Similarity=0.522 Sum_probs=33.5
Q ss_pred ccccccccccccc---CCceEEe-CCCCcccHhhHHHHHh-cCCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVNV---GETATKL-PCGHVYHGDCIVPWLD-SRNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~~---~e~~~~L-PC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~ 329 (363)
...|.||-+++.. |+.-+.. -|+--.|+.|..-=-+ .++.||.|+....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 4579999998763 3333333 3888899999832222 3568999998776
No 239
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=35.44 E-value=24 Score=25.17 Aligned_cols=35 Identities=14% Similarity=0.418 Sum_probs=24.1
Q ss_pred ccccccccccccCC-ceEEeCCCCcccHhhHHHHHh
Q 017955 282 IVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLD 316 (363)
Q Consensus 282 ~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk 316 (363)
..|.+|...|..-. ......||++||..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 46999988777422 122234999999999876654
No 240
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=35.44 E-value=12 Score=41.64 Aligned_cols=54 Identities=19% Similarity=0.327 Sum_probs=37.6
Q ss_pred CCCCCCCCCCC---CCCceeeeecCCcceeeecc--------CCCceecccCCCCceeeccCCCC
Q 017955 9 PTPTTPTASDT---DPTQYWCHHCEKRVSIETLA--------NLPDVICHECKNGFVESIPVTLT 62 (363)
Q Consensus 9 ~~~~~~~~~~~---~~~~~~C~~C~~~~~~~~~~--------~~~~~~c~~C~~gFve~~~~~~~ 62 (363)
..||.+++... -..+++|+.|.|+|+..... .---+.|..|+.+|+...+...+
T Consensus 862 ~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvH 926 (958)
T KOG1074|consen 862 GVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVH 926 (958)
T ss_pred cccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhh
Confidence 34444444333 34579999999999876332 22229999999999999877665
No 241
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.08 E-value=19 Score=29.36 Aligned_cols=13 Identities=15% Similarity=0.723 Sum_probs=11.4
Q ss_pred cccHhhHHHHHhc
Q 017955 305 VYHGDCIVPWLDS 317 (363)
Q Consensus 305 ~Fh~~CI~~WLk~ 317 (363)
-||+.|+..|++.
T Consensus 42 gFCRNCLs~Wy~e 54 (104)
T COG3492 42 GFCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999975
No 242
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=34.87 E-value=20 Score=24.37 Aligned_cols=24 Identities=38% Similarity=0.948 Sum_probs=16.2
Q ss_pred eeecCCcceeeeccCCCceecccCCCCcee
Q 017955 26 CHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
|+.|.+.+.+- -++|.+|++-|=.
T Consensus 1 C~~C~~~~~l~------~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLT------GFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCccccc------CeECCccCCcccc
Confidence 77888433321 3779999998853
No 243
>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=34.45 E-value=25 Score=24.84 Aligned_cols=40 Identities=28% Similarity=0.617 Sum_probs=22.2
Q ss_pred ccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
|..|...+.....+ ...-+..||..|+ +|-.|+..|....
T Consensus 1 C~~C~~~I~~~~~~-~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIV-IKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEE-EEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEE-EEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 55566665533222 1235667776664 5777777665543
No 244
>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=34.32 E-value=19 Score=24.33 Aligned_cols=24 Identities=25% Similarity=0.443 Sum_probs=18.2
Q ss_pred ceeeeecCCcceeeeccCCCceecccCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
.-||..|.+.++... +.+.|..|+
T Consensus 11 ~~~C~~C~~~i~~~~----~~~~C~~C~ 34 (49)
T smart00109 11 PTKCCVCRKSIWGSF----QGLRCSWCK 34 (49)
T ss_pred CCCccccccccCcCC----CCcCCCCCC
Confidence 458999997776532 679999995
No 245
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=34.31 E-value=37 Score=33.80 Aligned_cols=46 Identities=9% Similarity=-0.013 Sum_probs=34.1
Q ss_pred ccccccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFELPT 330 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l~~ 330 (363)
....|-+|-.... .....+|+| .||..|.. +....+||+|...+.+
T Consensus 342 s~~~~~~~~~~~~---st~~~~~~~n~~~~~~a~--~s~~~~~~~c~~~~~~ 388 (394)
T KOG2113|consen 342 SSLKGTSAGFGLL---STIWSGGNMNLSPGSLAS--ASASPTSSTCDHNDHT 388 (394)
T ss_pred hhcccccccCcee---eeEeecCCcccChhhhhh--cccCCcccccccccee
Confidence 4567888876654 345567998 89999987 6667799999876543
No 246
>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=34.29 E-value=12 Score=27.01 Aligned_cols=13 Identities=31% Similarity=0.859 Sum_probs=7.0
Q ss_pred CCCCcCcCCCCCC
Q 017955 320 TCPVCRFELPTDD 332 (363)
Q Consensus 320 sCPlCR~~l~~~d 332 (363)
.||+|.++|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999886544
No 247
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=34.09 E-value=34 Score=27.68 Aligned_cols=44 Identities=25% Similarity=0.523 Sum_probs=32.9
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHH
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYE 336 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~ 336 (363)
-..|+-|...+.--+ .+| |.-|+..+..|..|+++++..-+..|
T Consensus 33 rS~C~~C~~~L~~~~---lIP---------i~S~l~lrGrCr~C~~~I~~~y~l~E 76 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWD---LIP---------ILSYLLLRGRCRYCGAPIPPRYPLIE 76 (92)
T ss_pred CCcCcCCCCcCcccc---cch---------HHHHHHhCCCCcccCCCCChHHHHHH
Confidence 367999988877322 233 67899999999999999987655444
No 248
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=33.91 E-value=20 Score=35.65 Aligned_cols=7 Identities=14% Similarity=0.586 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 017955 85 LQVLRLI 91 (363)
Q Consensus 85 ~~~~~~~ 91 (363)
+++++-|
T Consensus 28 i~l~Rev 34 (324)
T PF05285_consen 28 INLFREV 34 (324)
T ss_pred HHHHHHH
Confidence 3333333
No 249
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=33.80 E-value=12 Score=41.44 Aligned_cols=70 Identities=19% Similarity=0.348 Sum_probs=40.6
Q ss_pred cccccccccccccccc------------CCceEEeC-CCCcccHh----------hHHHHHhcCCCCC---CcCcCCCCC
Q 017955 278 EQETIVCAICKDTVNV------------GETATKLP-CGHVYHGD----------CIVPWLDSRNTCP---VCRFELPTD 331 (363)
Q Consensus 278 ~~~~~~C~ICle~f~~------------~e~~~~LP-C~H~Fh~~----------CI~~WLk~~~sCP---lCR~~l~~~ 331 (363)
..+-.+|.||+..+.- |+.+.+.. |+.-|--. =+++-++...+|| +|-+++...
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccc
Confidence 3366789999987752 33444443 55444211 0112223345899 999988887
Q ss_pred ChhHHHHHHhhhccCC
Q 017955 332 DPEYEEERKKRVSAGA 347 (363)
Q Consensus 332 d~~~~~~~~~~~~~~~ 347 (363)
-...+..+.-...+..
T Consensus 682 V~lpQhIriH~~~~~s 697 (958)
T KOG1074|consen 682 VTLPQHIRIHLGGQIS 697 (958)
T ss_pred ccccceEEeecCCCCC
Confidence 7776666664444444
No 250
>PLN02436 cellulose synthase A
Probab=33.70 E-value=37 Score=39.01 Aligned_cols=49 Identities=22% Similarity=0.476 Sum_probs=34.3
Q ss_pred cccccccccccc---cCCceEEeC-CCCcccHhhHHHHHhc-CCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVN---VGETATKLP-CGHVYHGDCIVPWLDS-RNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~---~~e~~~~LP-C~H~Fh~~CI~~WLk~-~~sCPlCR~~l~ 329 (363)
...|.||-+++. .|+.-+... |+--.|+.|..-=.+. +++||.|+....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 457999999864 344444444 8888999998433333 568999998776
No 251
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=33.62 E-value=24 Score=38.70 Aligned_cols=12 Identities=50% Similarity=0.913 Sum_probs=7.3
Q ss_pred cCcCCCCCChhH
Q 017955 324 CRFELPTDDPEY 335 (363)
Q Consensus 324 CR~~l~~~d~~~ 335 (363)
|-..|..+||..
T Consensus 471 ~G~~LRkDDp~a 482 (822)
T KOG2141|consen 471 CGFSLRKDDPLA 482 (822)
T ss_pred ccchhcCCChHH
Confidence 556666666654
No 252
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.56 E-value=14 Score=26.64 Aligned_cols=15 Identities=53% Similarity=1.081 Sum_probs=12.4
Q ss_pred cCCCceecccCCCCc
Q 017955 39 ANLPDVICHECKNGF 53 (363)
Q Consensus 39 ~~~~~~~c~~C~~gF 53 (363)
..||+-|||-|+.-|
T Consensus 8 a~lp~KICpvCqRPF 22 (54)
T COG4338 8 ATLPDKICPVCQRPF 22 (54)
T ss_pred cccchhhhhhhcCch
Confidence 457899999998877
No 253
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=33.35 E-value=17 Score=39.19 Aligned_cols=27 Identities=37% Similarity=1.061 Sum_probs=21.4
Q ss_pred CCCCcccHhhHHHHHhcC---C--CCCCcCcC
Q 017955 301 PCGHVYHGDCIVPWLDSR---N--TCPVCRFE 327 (363)
Q Consensus 301 PC~H~Fh~~CI~~WLk~~---~--sCPlCR~~ 327 (363)
.|+-.||..|+.-|+... + .||-||.-
T Consensus 40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvC 71 (694)
T KOG4443|consen 40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVC 71 (694)
T ss_pred hhcccCCcchhhHHHhHHHhcCCcccCCceee
Confidence 488999999999998653 2 58888763
No 254
>PLN02189 cellulose synthase
Probab=33.25 E-value=39 Score=38.69 Aligned_cols=49 Identities=24% Similarity=0.518 Sum_probs=34.2
Q ss_pred cccccccccccc---cCCceEEeC-CCCcccHhhHHHHHhc-CCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVN---VGETATKLP-CGHVYHGDCIVPWLDS-RNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~---~~e~~~~LP-C~H~Fh~~CI~~WLk~-~~sCPlCR~~l~ 329 (363)
...|.||-+.+. .|+.-+... |+--.|+.|..-=-+. +++||.|+....
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 457999999876 333333334 8888999998433333 568999998776
No 255
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=33.15 E-value=34 Score=27.92 Aligned_cols=33 Identities=21% Similarity=0.487 Sum_probs=23.1
Q ss_pred ccccccccccccccCCceEEeC--CCCcccHhhHHHH
Q 017955 280 ETIVCAICKDTVNVGETATKLP--CGHVYHGDCIVPW 314 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LP--C~H~Fh~~CI~~W 314 (363)
....|.||.... |..+.... |...||..|...+
T Consensus 54 ~~~~C~iC~~~~--G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKSG--GACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCCC--ceeEEcCCCCCCcCCCHHHHHHC
Confidence 357899999873 33333333 8889999998663
No 256
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=33.04 E-value=20 Score=39.26 Aligned_cols=13 Identities=23% Similarity=0.266 Sum_probs=5.7
Q ss_pred CCCceeeccCCCC
Q 017955 50 KNGFVESIPVTLT 62 (363)
Q Consensus 50 ~~gFve~~~~~~~ 62 (363)
..|.|+.+-+.+.
T Consensus 102 ~~~~ve~~~e~s~ 114 (822)
T KOG2141|consen 102 RKGIVERSVEESK 114 (822)
T ss_pred cchHHHHHHHhcc
Confidence 3444554444333
No 257
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=33.02 E-value=62 Score=24.07 Aligned_cols=45 Identities=24% Similarity=0.475 Sum_probs=30.5
Q ss_pred cccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955 283 VCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329 (363)
Q Consensus 283 ~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~ 329 (363)
.|-.|-.++.... ...+-.=...||..|....| ++.||.|.-.|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccc
Confidence 4667777766443 33332223479999998866 789999987764
No 258
>PHA00626 hypothetical protein
Probab=32.87 E-value=32 Score=25.59 Aligned_cols=31 Identities=19% Similarity=0.515 Sum_probs=19.4
Q ss_pred eeeecCCc-cee-eeccC-CCceecccCCCCcee
Q 017955 25 WCHHCEKR-VSI-ETLAN-LPDVICHECKNGFVE 55 (363)
Q Consensus 25 ~C~~C~~~-~~~-~~~~~-~~~~~c~~C~~gFve 55 (363)
.|..|... |.. .+... ...|+|+.|+--|-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 37778742 222 23334 688999999877643
No 259
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=32.02 E-value=24 Score=26.14 Aligned_cols=21 Identities=24% Similarity=0.707 Sum_probs=14.3
Q ss_pred eeeecCCcceeeeccCCCceecccCC
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
+|.+|.+.. +.-..+.||+|+
T Consensus 1 ~Cpv~~~~~-----~~~v~~~Cp~cG 21 (55)
T PF13824_consen 1 LCPVCKKDL-----PAHVNFECPDCG 21 (55)
T ss_pred CCCCCcccc-----ccccCCcCCCCC
Confidence 366676332 555679999997
No 260
>PRK01343 zinc-binding protein; Provisional
Probab=31.69 E-value=26 Score=26.06 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=14.7
Q ss_pred eccCCCceecccCCCCce
Q 017955 37 TLANLPDVICHECKNGFV 54 (363)
Q Consensus 37 ~~~~~~~~~c~~C~~gFv 54 (363)
+.+.+|-+.||.|++-|+
T Consensus 3 ~~~~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 3 VEPLRPTRPCPECGKPST 20 (57)
T ss_pred cccCCCCCcCCCCCCcCc
Confidence 456678899999999875
No 261
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.49 E-value=16 Score=24.80 Aligned_cols=12 Identities=33% Similarity=1.085 Sum_probs=5.1
Q ss_pred CceeeeecCCcc
Q 017955 22 TQYWCHHCEKRV 33 (363)
Q Consensus 22 ~~~~C~~C~~~~ 33 (363)
++|||.-|.+.|
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 489999999544
No 262
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.47 E-value=29 Score=36.54 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=17.3
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
.++..||.|...... + ..||.|++.-+..
T Consensus 238 ~~~l~Ch~Cg~~~~~---~----~~Cp~C~s~~l~~ 266 (505)
T TIGR00595 238 EGKLRCHYCGYQEPI---P----KTCPQCGSEDLVY 266 (505)
T ss_pred CCeEEcCCCcCcCCC---C----CCCCCCCCCeeEe
Confidence 456678888822111 1 3599998865443
No 263
>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=31.38 E-value=26 Score=26.13 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=16.3
Q ss_pred eeecCCcceeeeccCCCceecccCCC
Q 017955 26 CHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
|+.|...+.. .+.-..++||.|+-
T Consensus 31 C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 31 CPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccccccc--ccccceEEcCCCCC
Confidence 8888844444 34456789999864
No 264
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.21 E-value=28 Score=38.12 Aligned_cols=29 Identities=21% Similarity=0.582 Sum_probs=19.1
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~ 57 (363)
..+..||.|.. .. +...||.|++..+..+
T Consensus 408 ~~~l~Ch~CG~----~~----~p~~Cp~Cgs~~l~~~ 436 (665)
T PRK14873 408 GGTPRCRWCGR----AA----PDWRCPRCGSDRLRAV 436 (665)
T ss_pred CCeeECCCCcC----CC----cCccCCCCcCCcceee
Confidence 45678999982 21 2347999988765544
No 265
>PF12773 DZR: Double zinc ribbon
Probab=31.20 E-value=22 Score=24.84 Aligned_cols=28 Identities=21% Similarity=0.623 Sum_probs=18.3
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCC
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
...-||.+|...+. ......++||.|+.
T Consensus 10 ~~~~fC~~CG~~l~---~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP---PPDQSKKICPNCGA 37 (50)
T ss_pred ccccCChhhcCChh---hccCCCCCCcCCcC
Confidence 34568999985555 22334578999987
No 266
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.07 E-value=27 Score=29.33 Aligned_cols=46 Identities=22% Similarity=0.397 Sum_probs=28.2
Q ss_pred cccccccccccccc--CCceEEeCCCCcccHhhHHHHHhcCC--CCCCcCc
Q 017955 280 ETIVCAICKDTVNV--GETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRF 326 (363)
Q Consensus 280 ~~~~C~ICle~f~~--~e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlCR~ 326 (363)
....|.+|...|.. +......-|+|.+|..|-.. ..... .|-+|.+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 45689999987752 23455556999999999655 11122 4777743
No 267
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.57 E-value=22 Score=21.85 Aligned_cols=23 Identities=22% Similarity=0.627 Sum_probs=14.1
Q ss_pred eeeeecCCcceeeeccCCCceecccCCCC
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
-.|..|.+ .+.. .+..||+|+.-
T Consensus 3 ~~Cp~Cg~----~~~~--~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGA----EIDP--DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCC----cCCc--ccccChhhCCC
Confidence 36888883 2222 24668888853
No 268
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=29.61 E-value=26 Score=40.98 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=23.8
Q ss_pred CCceeeeecCCcceee-----eccCCCceecccCCCCce
Q 017955 21 PTQYWCHHCEKRVSIE-----TLANLPDVICHECKNGFV 54 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~-----~~~~~~~~~c~~C~~gFv 54 (363)
.++|+|-+|...-+.+ .--+||+-.||.|+.-++
T Consensus 681 ~phy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~~~ 719 (1213)
T TIGR01405 681 PPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719 (1213)
T ss_pred cccccCcccccccccccccccccccCccccCcccccccc
Confidence 4589999998433332 123589999999987544
No 269
>PRK11032 hypothetical protein; Provisional
Probab=29.55 E-value=39 Score=30.34 Aligned_cols=32 Identities=22% Similarity=0.500 Sum_probs=24.8
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
..+.+-|-+|...+.......+|. ||.|++.-
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~i~p--Cp~C~~~~ 152 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEVLPL--CPKCGHDQ 152 (160)
T ss_pred ecceEEecCCCCEEEecCCCcCCC--CCCCCCCe
Confidence 467899999997777776666643 99999863
No 270
>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=29.51 E-value=34 Score=21.52 Aligned_cols=29 Identities=21% Similarity=0.471 Sum_probs=10.3
Q ss_pred cccccccccccCCceEEeCCCCcccHhhH
Q 017955 283 VCAICKDTVNVGETATKLPCGHVYHGDCI 311 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI 311 (363)
.|.+|......+-.-....|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 48888887664223444558889999886
No 271
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=29.36 E-value=18 Score=42.74 Aligned_cols=49 Identities=27% Similarity=0.490 Sum_probs=37.8
Q ss_pred ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCcCC
Q 017955 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRFEL 328 (363)
Q Consensus 280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~~l 328 (363)
....|.||+........+.+.-|.-.||..|+.+-+.... .||-||..-
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 4567999999877544455555889999999999887654 799998754
No 272
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=29.36 E-value=31 Score=28.58 Aligned_cols=15 Identities=20% Similarity=0.696 Sum_probs=12.9
Q ss_pred CCCceecccCCCCce
Q 017955 40 NLPDVICHECKNGFV 54 (363)
Q Consensus 40 ~~~~~~c~~C~~gFv 54 (363)
..|-++|+.|+..|+
T Consensus 28 ~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 28 GVPGWYCPACGEELL 42 (127)
T ss_pred eeeeeECCCCCCEEE
Confidence 678899999998765
No 273
>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=29.30 E-value=29 Score=26.93 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=13.8
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCC
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
..+|.|-.|.+.+...-. ||.|+.
T Consensus 15 ~~~~~C~~C~~~~~~~a~-------CPdC~~ 38 (70)
T PF07191_consen 15 GGHYHCEACQKDYKKEAF-------CPDCGQ 38 (70)
T ss_dssp TTEEEETTT--EEEEEEE--------TTT-S
T ss_pred CCEEECccccccceeccc-------CCCccc
Confidence 368888888876666543 777764
No 274
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=29.17 E-value=31 Score=24.26 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=19.2
Q ss_pred CceeeeecCCcceeeeccCCCceecccCCC
Q 017955 22 TQYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 22 ~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
..-||..|.+.++. ...+.+.|..|+-
T Consensus 10 ~~~~C~~C~~~i~g---~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG---LGKQGYRCSWCGL 36 (53)
T ss_dssp STEB-TTSSSBECS---SSSCEEEETTTT-
T ss_pred CCCCCcccCcccCC---CCCCeEEECCCCC
Confidence 35599999977744 5567899999974
No 275
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=29.09 E-value=36 Score=33.12 Aligned_cols=38 Identities=21% Similarity=0.454 Sum_probs=29.6
Q ss_pred CCCCCceeeeecCCcceeeec----------cC-CCceecccCCCCcee
Q 017955 18 DTDPTQYWCHHCEKRVSIETL----------AN-LPDVICHECKNGFVE 55 (363)
Q Consensus 18 ~~~~~~~~C~~C~~~~~~~~~----------~~-~~~~~c~~C~~gFve 55 (363)
+....+|-|-.|.|..++... .. -....|++|++-||-
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVS 173 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccccccccccCCCCCceeee
Confidence 447889999999998888763 11 356899999998873
No 276
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.02 E-value=56 Score=26.91 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=29.8
Q ss_pred cccccccccccccCCceEEeCCCCcccHhhHHHHHhc
Q 017955 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS 317 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~ 317 (363)
.+.|.||-..+..|+..+-.+ +-..|.+|+..-..+
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~ 41 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRK 41 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhc
Confidence 367999999999999888888 666899999876543
No 277
>PLN02400 cellulose synthase
Probab=29.02 E-value=40 Score=38.78 Aligned_cols=49 Identities=24% Similarity=0.523 Sum_probs=33.4
Q ss_pred ccccccccccccc---CCc-eEEeCCCCcccHhhHHHHHh-cCCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVNV---GET-ATKLPCGHVYHGDCIVPWLD-SRNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~~---~e~-~~~LPC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~ 329 (363)
...|.||-+++.. |+. +.+--|+--.|+.|..-=-+ .+++||.|+....
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 4579999998763 332 33334888899999832122 2558999998776
No 278
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=28.82 E-value=44 Score=33.90 Aligned_cols=14 Identities=21% Similarity=0.285 Sum_probs=7.9
Q ss_pred CCCCcCcCCCCCCh
Q 017955 320 TCPVCRFELPTDDP 333 (363)
Q Consensus 320 sCPlCR~~l~~~d~ 333 (363)
.||+=..+-.+-||
T Consensus 295 ~C~iTg~PA~Y~DP 308 (390)
T KOG2897|consen 295 VCVITGRPARYLDP 308 (390)
T ss_pred cccccCCcccccCc
Confidence 57766655554443
No 279
>PLN02195 cellulose synthase A
Probab=28.79 E-value=62 Score=36.87 Aligned_cols=49 Identities=24% Similarity=0.487 Sum_probs=33.8
Q ss_pred ccccccccccccc---CCc-eEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCC
Q 017955 281 TIVCAICKDTVNV---GET-ATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELP 329 (363)
Q Consensus 281 ~~~C~ICle~f~~---~e~-~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~ 329 (363)
...|.||-+.+.. |+. +.+--|+--.|+.|..-=-+. ++.||.|+....
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 4579999987653 333 333348888999998332222 558999999887
No 280
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=28.41 E-value=37 Score=32.29 Aligned_cols=31 Identities=16% Similarity=0.391 Sum_probs=23.4
Q ss_pred CcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955 304 HVYHGDCIVPWLDSRNTCPVCRFELPTDDPE 334 (363)
Q Consensus 304 H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~ 334 (363)
-.-|.+|-.+.-++...||+|+..--..+|.
T Consensus 249 MK~ClsChqqIHRNAPiCPlCKaKsRSrNPK 279 (286)
T KOG4451|consen 249 MKVCLSCHQQIHRNAPICPLCKAKSRSRNPK 279 (286)
T ss_pred chHHHHHHHHHhcCCCCCcchhhccccCCCC
Confidence 3467778777778888999998877666654
No 281
>PHA00733 hypothetical protein
Probab=27.90 E-value=24 Score=30.22 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=25.2
Q ss_pred CCceeeeecCCcceeeeccC------CCceecccCCCCceee
Q 017955 21 PTQYWCHHCEKRVSIETLAN------LPDVICHECKNGFVES 56 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~------~~~~~c~~C~~gFve~ 56 (363)
...|-|-.|.+.|+...... ..-+.|+.|+..|...
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNT 112 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCH
Confidence 45688999998877654321 1247999999998754
No 282
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.41 E-value=37 Score=37.06 Aligned_cols=45 Identities=38% Similarity=0.731 Sum_probs=33.6
Q ss_pred cccccccccccCCceEEeCCCC-cccHhhHHHHH--hc----CCCCCCcCcCCCC
Q 017955 283 VCAICKDTVNVGETATKLPCGH-VYHGDCIVPWL--DS----RNTCPVCRFELPT 330 (363)
Q Consensus 283 ~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WL--k~----~~sCPlCR~~l~~ 330 (363)
.|+||-..+. .+..-.|+| .-|..|..... .. .+.||+||..+..
T Consensus 2 ~c~ic~~s~~---~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 2 SCAICAFSPD---FVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred CcceeecCcc---ccccccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 4999988765 445556999 99999998874 23 4578999996644
No 283
>PRK10220 hypothetical protein; Provisional
Probab=27.22 E-value=36 Score=28.64 Aligned_cols=27 Identities=30% Similarity=0.690 Sum_probs=20.0
Q ss_pred eeecCCcceee-eccCCCceecccCCCCceee
Q 017955 26 CHHCEKRVSIE-TLANLPDVICHECKNGFVES 56 (363)
Q Consensus 26 C~~C~~~~~~~-~~~~~~~~~c~~C~~gFve~ 56 (363)
|.+|. -+ +-..-..+|||.|..-|-.+
T Consensus 6 CP~C~----seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCN----SEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred CCCCC----CcceEcCCCeEECCcccCcCCcc
Confidence 88898 44 55555669999999877644
No 284
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.17 E-value=24 Score=25.87 Aligned_cols=23 Identities=30% Similarity=0.872 Sum_probs=17.3
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
--.|..|. ...+|-.+|+.| ||.
T Consensus 26 l~~c~~cg-------~~~~~H~vc~~c--G~y 48 (56)
T PF01783_consen 26 LVKCPNCG-------EPKLPHRVCPSC--GYY 48 (56)
T ss_dssp EEESSSSS-------SEESTTSBCTTT--BBS
T ss_pred eeeeccCC-------CEecccEeeCCC--CeE
Confidence 45688888 466788899999 464
No 285
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.80 E-value=30 Score=35.38 Aligned_cols=32 Identities=22% Similarity=0.478 Sum_probs=27.2
Q ss_pred CCCceeeeecCCcceeeeccCCCceecccCCC
Q 017955 20 DPTQYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
..+.--|-.|.+.|.+-...--+..-||+|+-
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~ 46 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGH 46 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCC
Confidence 35566799999999998888888999999985
No 286
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=26.38 E-value=29 Score=39.29 Aligned_cols=9 Identities=0% Similarity=0.320 Sum_probs=3.8
Q ss_pred HHHHHHHHh
Q 017955 244 ALLQNLAES 252 (363)
Q Consensus 244 ~Ll~~L~~~ 252 (363)
.+++.+..+
T Consensus 435 ~iVkai~~q 443 (1233)
T KOG1824|consen 435 LIVKAIQKQ 443 (1233)
T ss_pred HHHHHHHHH
Confidence 344444443
No 287
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=26.26 E-value=41 Score=31.99 Aligned_cols=26 Identities=19% Similarity=0.546 Sum_probs=19.3
Q ss_pred ccccccccccccCCceEEeCCCCccc
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYH 307 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh 307 (363)
..||||...+.......+.+.+|.|-
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~fd 28 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQFD 28 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCCc
Confidence 47999999997655555556689883
No 288
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=26.10 E-value=35 Score=28.65 Aligned_cols=28 Identities=25% Similarity=0.629 Sum_probs=20.0
Q ss_pred eeecCCcceeeeccCCCceecccCCCCceee
Q 017955 26 CHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
|.+|.... +-..-.-+|||.|.--|...
T Consensus 5 CP~C~sey---tY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEY---TYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcc---eEecCCeeECcccccccccc
Confidence 88898222 44555669999999888655
No 290
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=25.95 E-value=47 Score=31.52 Aligned_cols=29 Identities=17% Similarity=0.483 Sum_probs=21.6
Q ss_pred ccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955 306 YHGDCIVPWLDSRNTCPVCRFELPTDDPE 334 (363)
Q Consensus 306 Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~ 334 (363)
-|.+|-..--++...||+|+..--..+|.
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~KsRSrnpK 224 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKSRSRNPK 224 (230)
T ss_pred hhHhHHHHHhcCCCCCcccccccccCCCC
Confidence 46777777667888999998876665553
No 291
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=25.90 E-value=55 Score=27.19 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=27.3
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD 316 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk 316 (363)
+.|.||-+.+..|+.-+-++= -.-|+.|+..=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHHHHHHh
Confidence 679999999998887776654 6689999987553
No 292
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.63 E-value=39 Score=23.59 Aligned_cols=16 Identities=44% Similarity=0.914 Sum_probs=13.1
Q ss_pred cCCCceecccCCCCce
Q 017955 39 ANLPDVICHECKNGFV 54 (363)
Q Consensus 39 ~~~~~~~c~~C~~gFv 54 (363)
..||.-+|+.|+--|.
T Consensus 4 ~~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 4 SNLPSKICPVCGRPFT 19 (42)
T ss_pred ccCCCCcCcccCCcch
Confidence 4688899999998773
No 293
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=25.26 E-value=32 Score=29.75 Aligned_cols=18 Identities=28% Similarity=0.608 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeeeecC
Q 017955 13 TPTASDTDPTQYWCHHCE 30 (363)
Q Consensus 13 ~~~~~~~~~~~~~C~~C~ 30 (363)
..+|+..+..+|+||.|.
T Consensus 18 A~~a~~~~~~~~tC~~Cg 35 (128)
T PF11682_consen 18 ARTAASAPYDHWTCHSCG 35 (128)
T ss_pred hhhhhhCCCCeEEEecCC
Confidence 345667788999999999
No 294
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=24.78 E-value=57 Score=33.92 Aligned_cols=42 Identities=24% Similarity=0.511 Sum_probs=29.7
Q ss_pred ceeeecccccccccccccccccCCc--eEEeCCCCcccHhhHHHH
Q 017955 272 TVEILSEQETIVCAICKDTVNVGET--ATKLPCGHVYHGDCIVPW 314 (363)
Q Consensus 272 ~~~~~~~~~~~~C~ICle~f~~~e~--~~~LPC~H~Fh~~CI~~W 314 (363)
.+....+.....||+|-+.|..-.. -++| ||-+.|.+|.+..
T Consensus 171 vVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRL-CG~VmC~~C~k~i 214 (505)
T KOG1842|consen 171 VVPWLDDSSVQFCPECANSFGLTRRRHHCRL-CGRVMCRDCSKFI 214 (505)
T ss_pred cccccCCCcccccccccchhhhHHHhhhhhh-cchHHHHHHHHhc
Confidence 4555556678889999999974321 1223 9999999997654
No 295
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.56 E-value=37 Score=22.77 Aligned_cols=10 Identities=40% Similarity=0.983 Sum_probs=8.0
Q ss_pred ceecccCCCC
Q 017955 43 DVICHECKNG 52 (363)
Q Consensus 43 ~~~c~~C~~g 52 (363)
++.||+|++.
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 4789999874
No 296
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=24.14 E-value=49 Score=35.30 Aligned_cols=12 Identities=25% Similarity=0.146 Sum_probs=8.0
Q ss_pred CCceeeccCCCC
Q 017955 51 NGFVESIPVTLT 62 (363)
Q Consensus 51 ~gFve~~~~~~~ 62 (363)
=|||-||..++.
T Consensus 141 ~G~V~Ei~IP~k 152 (678)
T KOG0127|consen 141 FGKVVEIVIPRK 152 (678)
T ss_pred cceEEEEEcccC
Confidence 477777776643
No 297
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.10 E-value=50 Score=25.88 Aligned_cols=47 Identities=21% Similarity=0.420 Sum_probs=29.5
Q ss_pred ccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 284 CAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 284 C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
|--|-.++..+. ...+..=.|.||.+|... +.+..||.|-..|...-
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~--~l~g~CPnCGGelv~RP 55 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAEN--RLHGLCPNCGGELVARP 55 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHH--hhcCcCCCCCchhhcCc
Confidence 545555554332 222222257899999876 45789999988775443
No 298
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.08 E-value=27 Score=27.67 Aligned_cols=32 Identities=19% Similarity=0.558 Sum_probs=24.4
Q ss_pred eeeecCCcceeee------ccCCCceecccC--CCCceee
Q 017955 25 WCHHCEKRVSIET------LANLPDVICHEC--KNGFVES 56 (363)
Q Consensus 25 ~C~~C~~~~~~~~------~~~~~~~~c~~C--~~gFve~ 56 (363)
+|-.|.|++.... +.....--|.+| +++|++.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~~ 41 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQD 41 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceeec
Confidence 6889998888777 555667778888 5677773
No 299
>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=23.98 E-value=25 Score=25.62 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=19.7
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
-+-|-+|.|-+-..-.-.-=.+.||+|+.=+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 5778999866554211112358899998744
No 300
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=23.85 E-value=60 Score=28.22 Aligned_cols=40 Identities=18% Similarity=0.311 Sum_probs=27.7
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCceeeccCCCCCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPP 64 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~~~~~ 64 (363)
.|-|-+|.+-|.-....-| -=||.|++.+-+=++......
T Consensus 1 PH~Ct~Cg~~f~dgs~eil--~GCP~CGg~kF~yv~~~~~~~ 40 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEIL--SGCPECGGNKFQYVPEEKDAE 40 (131)
T ss_pred CcccCcCCCCcCCCcHHHH--ccCcccCCcceEEcCCCcccc
Confidence 3789999976654432222 239999999988887765533
No 301
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=23.76 E-value=47 Score=31.42 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=9.8
Q ss_pred eecccCCCCcee
Q 017955 44 VICHECKNGFVE 55 (363)
Q Consensus 44 ~~c~~C~~gFve 55 (363)
+.|.|=+.-||.
T Consensus 97 lsc~Y~g~eFvR 108 (279)
T COG5137 97 LSCRYKGQEFVR 108 (279)
T ss_pred EEEeecCceeEE
Confidence 568888888886
No 302
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=23.72 E-value=26 Score=34.80 Aligned_cols=45 Identities=18% Similarity=0.202 Sum_probs=32.9
Q ss_pred cccccccccccccCCceEEeCCCC-cccHhhHHHH-HhcCCCCCCcCcCC
Q 017955 281 TIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPW-LDSRNTCPVCRFEL 328 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~W-Lk~~~sCPlCR~~l 328 (363)
...|.+|+..-. .++..+|+| +||..|.-+- +++..+||+|-..+
T Consensus 136 ti~~iqq~tnt~---I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~ 182 (394)
T KOG2113|consen 136 TIKRIQQFTNTY---IATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAV 182 (394)
T ss_pred ccchheecccce---EeeeccCCCceEEEecCCcchhhhccccchhhhhh
Confidence 356888887533 455667998 8999997665 66777899997644
No 303
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.71 E-value=48 Score=28.81 Aligned_cols=28 Identities=21% Similarity=0.391 Sum_probs=21.5
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNGFV 54 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv 54 (363)
-+-|..|..+.+. +--+++||-|+.-|+
T Consensus 28 ~~hCp~Cg~PLF~----KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTPLFR----KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCccee----eCCeEECCCCCceEE
Confidence 4679999966665 667899999996443
No 304
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.46 E-value=52 Score=28.32 Aligned_cols=25 Identities=16% Similarity=0.518 Sum_probs=19.9
Q ss_pred eeecCCcceeeeccCCCceecccCC
Q 017955 26 CHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 26 C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
|+-|.+.-.+...-......||+|+
T Consensus 3 C~fC~~~s~~~~~~~~~~w~C~~C~ 27 (131)
T PF09779_consen 3 CWFCGQNSKVPYDNRNSNWTCPHCE 27 (131)
T ss_pred eccCCCCCCCCCCCCCCeeECCCCC
Confidence 8888877667666667779999996
No 305
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.40 E-value=34 Score=24.62 Aligned_cols=11 Identities=36% Similarity=1.159 Sum_probs=8.9
Q ss_pred ecccCCCCcee
Q 017955 45 ICHECKNGFVE 55 (363)
Q Consensus 45 ~c~~C~~gFve 55 (363)
.||.|+++|+-
T Consensus 22 fCP~Cg~~~m~ 32 (50)
T PRK00432 22 FCPRCGSGFMA 32 (50)
T ss_pred cCcCCCcchhe
Confidence 69999998544
No 306
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.37 E-value=24 Score=36.45 Aligned_cols=36 Identities=22% Similarity=0.469 Sum_probs=26.1
Q ss_pred cccccccccccCC-----ceEEeCCCCcccHhhHHHHHhcC
Q 017955 283 VCAICKDTVNVGE-----TATKLPCGHVYHGDCIVPWLDSR 318 (363)
Q Consensus 283 ~C~ICle~f~~~e-----~~~~LPC~H~Fh~~CI~~WLk~~ 318 (363)
.||.|.-.+.... .....+|+|.||.-|+..|....
T Consensus 228 ~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 228 ECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred cCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 4999998877443 12222599999999988887664
No 307
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=22.93 E-value=57 Score=30.73 Aligned_cols=11 Identities=9% Similarity=0.072 Sum_probs=7.3
Q ss_pred cchhccccCCC
Q 017955 113 DFLRIELDGWE 123 (363)
Q Consensus 113 ~f~~~~~~~~~ 123 (363)
.|++|.+....
T Consensus 178 yYfK~~K~K~~ 188 (218)
T PF14283_consen 178 YYFKFYKPKQE 188 (218)
T ss_pred EEEEEeccccc
Confidence 36777776654
No 308
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=22.88 E-value=37 Score=23.16 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=19.2
Q ss_pred ceeeeecCCcceeeeccCCCceecccCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
.-||..|.+.++.- ..+.+.|..|+
T Consensus 11 ~~~C~~C~~~i~~~---~~~~~~C~~C~ 35 (50)
T cd00029 11 PTFCDVCRKSIWGL---FKQGLRCSWCK 35 (50)
T ss_pred CCChhhcchhhhcc---ccceeEcCCCC
Confidence 45799999777652 45889999995
No 309
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=22.84 E-value=35 Score=30.97 Aligned_cols=27 Identities=15% Similarity=0.396 Sum_probs=9.2
Q ss_pred eeeeecCCcceeeeccCCCceecccCC
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECK 50 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~ 50 (363)
-.|-+|.-++-+.....-..++||.|+
T Consensus 135 ~~C~~C~~~fv~~~~~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 135 APCRRCGGHFVTHAHDPRHSFVCPFCQ 161 (175)
T ss_dssp EE-TTT--EEEEESS--SS----TT--
T ss_pred cCCCCCCCCeECcCCCCCcCcCCCCCC
Confidence 357777755555433334567777776
No 310
>PRK06260 threonine synthase; Validated
Probab=22.47 E-value=47 Score=33.63 Aligned_cols=25 Identities=24% Similarity=0.351 Sum_probs=18.1
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKN 51 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~ 51 (363)
+|.|..|. .+..+....+.||.|++
T Consensus 3 ~~~C~~cg----~~~~~~~~~~~Cp~cg~ 27 (397)
T PRK06260 3 WLKCIECG----KEYDPDEIIYTCPECGG 27 (397)
T ss_pred EEEECCCC----CCCCCCCccccCCCCCC
Confidence 58999999 44444444588999974
No 311
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.41 E-value=20 Score=35.45 Aligned_cols=45 Identities=16% Similarity=0.349 Sum_probs=28.3
Q ss_pred cccccccccccccCCceEE----eCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955 281 TIVCAICKDTVNVGETATK----LPCGHVYHGDCIVPWLDSRNTCPVCRF 326 (363)
Q Consensus 281 ~~~C~ICle~f~~~e~~~~----LPC~H~Fh~~CI~~WLk~~~sCPlCR~ 326 (363)
...||||-..-... .+.. --=.|.+|.-|-..|--.+..||.|-.
T Consensus 184 ~~~CPvCGs~P~~s-~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACGSPPVAS-MVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCcCCCCCChhhhh-hhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 45899997743211 0000 001355677788899888889999965
No 312
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=22.32 E-value=64 Score=33.12 Aligned_cols=50 Identities=24% Similarity=0.361 Sum_probs=39.7
Q ss_pred ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE 334 (363)
Q Consensus 282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~ 334 (363)
..|.+-|-.|. .++++.=+-+|-..-|++||+.+.+-|+=-+++...+..
T Consensus 41 ~hC~lt~~Pfe---~PvC~~dg~vFd~~~Ivp~lkk~g~nP~tG~kl~~~dLI 90 (518)
T KOG0883|consen 41 NHCSLTMLPFE---DPVCTVDGTVFDLTAIVPWLKKHGTNPITGQKLDGKDLI 90 (518)
T ss_pred hhceecccccc---CcccccCCcEEeeehhhHHHHHcCCCCCCCCccccccce
Confidence 45888777776 566677788999999999999988888877777666644
No 313
>PRK13795 hypothetical protein; Provisional
Probab=22.26 E-value=55 Score=35.59 Aligned_cols=29 Identities=24% Similarity=0.684 Sum_probs=20.3
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP 58 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~ 58 (363)
-+=|||..|+ +-+..+. |..|+++. .++.
T Consensus 10 ~~~~wc~~cn----~p~~~~~----c~~c~~~~-~~~~ 38 (636)
T PRK13795 10 DHIYWCEKCN----VPLLGKK----CGICGKEG-FKVR 38 (636)
T ss_pred eeEEEcccCC----Ceecccc----ccccCCCc-eEee
Confidence 3569999999 5544443 99999964 3443
No 314
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.25 E-value=45 Score=36.36 Aligned_cols=41 Identities=22% Similarity=0.429 Sum_probs=29.4
Q ss_pred ccccccccccc-cCCceEEeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955 282 IVCAICKDTVN-VGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325 (363)
Q Consensus 282 ~~C~ICle~f~-~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR 325 (363)
..|.||...=. .....+.+.|+-.||..| |+--++.||+|-
T Consensus 655 r~C~vcq~pedse~~v~rt~~C~~~~C~~c---~~~~~~~~~vC~ 696 (717)
T KOG3726|consen 655 RTCKVCQLPEDSETDVCRTTFCYTPYCVAC---SLDYASISEVCG 696 (717)
T ss_pred HHHHHhcCCcCccccccCccccCCcchHhh---hhhhhccCcccC
Confidence 56888876433 122445556999999998 777788899993
No 315
>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=22.16 E-value=62 Score=23.31 Aligned_cols=10 Identities=40% Similarity=1.013 Sum_probs=7.3
Q ss_pred ceecccCCCC
Q 017955 43 DVICHECKNG 52 (363)
Q Consensus 43 ~~~c~~C~~g 52 (363)
+.+||.|+.+
T Consensus 34 ~w~CP~C~a~ 43 (50)
T cd00730 34 DWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCc
Confidence 5788888754
No 316
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.16 E-value=54 Score=35.88 Aligned_cols=29 Identities=28% Similarity=0.603 Sum_probs=16.3
Q ss_pred CCceeeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
.....||.|...... ...||.|++-.+..
T Consensus 406 ~~~l~Ch~Cg~~~~~-------~~~Cp~Cg~~~l~~ 434 (679)
T PRK05580 406 QRRLRCHHCGYQEPI-------PKACPECGSTDLVP 434 (679)
T ss_pred CCeEECCCCcCCCCC-------CCCCCCCcCCeeEE
Confidence 445677777722111 13488888765443
No 317
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.86 E-value=20 Score=31.29 Aligned_cols=58 Identities=22% Similarity=0.354 Sum_probs=28.0
Q ss_pred ccccccccccccc-cCCceEEeCCCCcccHhhHHHH-HhcCC---CCCCcCcCC--CCCChhHHH
Q 017955 280 ETIVCAICKDTVN-VGETATKLPCGHVYHGDCIVPW-LDSRN---TCPVCRFEL--PTDDPEYEE 337 (363)
Q Consensus 280 ~~~~C~ICle~f~-~~e~~~~LPC~H~Fh~~CI~~W-Lk~~~---sCPlCR~~l--~~~d~~~~~ 337 (363)
.+-.|.||+..-. +|---...=|.-.||..|--+- |+.++ .|-+||+.. .++.-.|-+
T Consensus 64 ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~q~il~ksg~wf~ 128 (169)
T KOG3799|consen 64 DDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFY 128 (169)
T ss_pred cCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHHHHHHHhcchHHH
Confidence 5678999998532 2211111113334454553332 22233 688997643 344433433
No 318
>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=21.79 E-value=49 Score=26.85 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=17.4
Q ss_pred eeeecCCcceeeeccCCCceecccCCCC
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
||..|. .-+.+....++|+.|+.-
T Consensus 2 fC~~Cg----~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCG----SLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccC----cccccCCCeEECcCCCCc
Confidence 799999 333444467999999853
No 319
>KOG1834 consensus Calsyntenin [Extracellular structures]
Probab=21.64 E-value=50 Score=36.01 Aligned_cols=8 Identities=13% Similarity=0.414 Sum_probs=3.6
Q ss_pred CceeeccC
Q 017955 52 GFVESIPV 59 (363)
Q Consensus 52 gFve~~~~ 59 (363)
-|+=+|+.
T Consensus 772 ef~vev~i 779 (952)
T KOG1834|consen 772 EFFVEVNI 779 (952)
T ss_pred eeEEEEEE
Confidence 34444443
No 320
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.40 E-value=34 Score=32.74 Aligned_cols=32 Identities=16% Similarity=0.295 Sum_probs=22.8
Q ss_pred CCCceeeeecCCcceee----eccCCCceecccCCC
Q 017955 20 DPTQYWCHHCEKRVSIE----TLANLPDVICHECKN 51 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~----~~~~~~~~~c~~C~~ 51 (363)
+-.-.-|.-|.|-++.. |.-+.+=|.||+|+.
T Consensus 194 pl~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 194 PLEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred eecCCcccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 34456799999777665 333467799999985
No 321
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=21.39 E-value=68 Score=32.37 Aligned_cols=64 Identities=27% Similarity=0.471 Sum_probs=34.2
Q ss_pred cccccccccccccccCCceEEe---CCCCccc--------HhhHHHHH-----hcCCCCCCcCcCCC-CCChhHHHHHHh
Q 017955 279 QETIVCAICKDTVNVGETATKL---PCGHVYH--------GDCIVPWL-----DSRNTCPVCRFELP-TDDPEYEEERKK 341 (363)
Q Consensus 279 ~~~~~C~ICle~f~~~e~~~~L---PC~H~Fh--------~~CI~~WL-----k~~~sCPlCR~~l~-~~d~~~~~~~~~ 341 (363)
..++.||||-+.... -.-..| .|+-.|. ..|+..-- .+++.||.||+.-+ +---..+.+|..
T Consensus 13 dl~ElCPVCGDkVSG-YHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRAD 91 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSG-YHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRAD 91 (475)
T ss_pred ccccccccccCcccc-ceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHh
Confidence 356789999887652 233333 3555443 23433211 12457999998532 333444555555
Q ss_pred hh
Q 017955 342 RV 343 (363)
Q Consensus 342 ~~ 343 (363)
|+
T Consensus 92 RM 93 (475)
T KOG4218|consen 92 RM 93 (475)
T ss_pred hh
Confidence 54
No 322
>PLN02248 cellulose synthase-like protein
Probab=21.33 E-value=75 Score=36.76 Aligned_cols=36 Identities=25% Similarity=0.515 Sum_probs=29.3
Q ss_pred eEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955 297 ATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 297 ~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d 332 (363)
+....|++..|++|...-++....||-|+.+....+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (1135)
T PLN02248 145 LLPCECGFKICRDCYIDAVKSGGICPGCKEPYKVTD 180 (1135)
T ss_pred CCcccccchhHHhHhhhhhhcCCCCCCCcccccccc
Confidence 333448899999999999999999999998875433
No 323
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.27 E-value=35 Score=20.82 Aligned_cols=12 Identities=33% Similarity=0.623 Sum_probs=9.6
Q ss_pred eecccCCCCcee
Q 017955 44 VICHECKNGFVE 55 (363)
Q Consensus 44 ~~c~~C~~gFve 55 (363)
+.||.|+..|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 579999988854
No 324
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.27 E-value=57 Score=24.46 Aligned_cols=30 Identities=13% Similarity=0.433 Sum_probs=17.4
Q ss_pred CCceeeeecCCc-ceee-eccC-CCceecccCC
Q 017955 21 PTQYWCHHCEKR-VSIE-TLAN-LPDVICHECK 50 (363)
Q Consensus 21 ~~~~~C~~C~~~-~~~~-~~~~-~~~~~c~~C~ 50 (363)
..+|.|-.|.+. +++= .=.+ .-.|+||.|+
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCceECCCCC
Confidence 557888888843 2211 1111 3568888885
No 325
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.26 E-value=25 Score=27.76 Aligned_cols=38 Identities=21% Similarity=0.552 Sum_probs=25.6
Q ss_pred CCCceeeeecCCcceee-eccCCCceecccCCCCceeec
Q 017955 20 DPTQYWCHHCEKRVSIE-TLANLPDVICHECKNGFVESI 57 (363)
Q Consensus 20 ~~~~~~C~~C~~~~~~~-~~~~~~~~~c~~C~~gFve~~ 57 (363)
+.-+|-|-.|.-.+-+- --.+.|-.+||.|+.-|-..|
T Consensus 9 PtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~~kk~l 47 (82)
T COG2331 9 PTYSYECTECGNRFDVVQAMTDDPLTTCEECGARLKKLL 47 (82)
T ss_pred cceEEeecccchHHHHHHhcccCccccChhhChHHHHhh
Confidence 35689999999555443 334568899999976444433
No 326
>PHA02768 hypothetical protein; Provisional
Probab=21.11 E-value=27 Score=25.77 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=23.9
Q ss_pred CceeeeecCCcceeeeccC------CCceecccCCCCce
Q 017955 22 TQYWCHHCEKRVSIETLAN------LPDVICHECKNGFV 54 (363)
Q Consensus 22 ~~~~C~~C~~~~~~~~~~~------~~~~~c~~C~~gFv 54 (363)
.-|-|..|.|.|+...... ..-+.|..|+..|-
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISL 42 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceec
Confidence 4688999998888775433 13568888888775
No 327
>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=20.98 E-value=54 Score=21.01 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=11.7
Q ss_pred ceeeeecCCcceeeeccCCCceecccCCCC
Q 017955 23 QYWCHHCEKRVSIETLANLPDVICHECKNG 52 (363)
Q Consensus 23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~g 52 (363)
+.+|..|. . ...|+||.|+.-
T Consensus 2 ~~~C~vC~----~-----~~kY~Cp~C~~~ 22 (30)
T PF04438_consen 2 RKLCSVCG----N-----PAKYRCPRCGAR 22 (30)
T ss_dssp -EEETSSS----S-----EESEE-TTT--E
T ss_pred cCCCccCc----C-----CCEEECCCcCCc
Confidence 56788888 2 334889988754
No 328
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=20.96 E-value=38 Score=27.07 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=19.4
Q ss_pred eeecCCcce------eeeccCCCceecccCCCC
Q 017955 26 CHHCEKRVS------IETLANLPDVICHECKNG 52 (363)
Q Consensus 26 C~~C~~~~~------~~~~~~~~~~~c~~C~~g 52 (363)
||||...|. ++|....-.+.|+=|..-
T Consensus 3 C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V 35 (88)
T PF12156_consen 3 CYHCGLPVPEGAKITVEIDGEERPFCCPGCQAV 35 (88)
T ss_pred CCCCCCCCCCCCCeeeeeCCCccccccHHHHHH
Confidence 999997774 445555567888888753
No 329
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=20.89 E-value=47 Score=32.16 Aligned_cols=53 Identities=23% Similarity=0.443 Sum_probs=0.0
Q ss_pred cccccccchhhccccCCcCCCCCCCCCCccccccCCCCCCCCccccccchhhh
Q 017955 125 DAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDE 177 (363)
Q Consensus 125 ~~~~~~~~~~ee~~~~~e~~d~~d~edddddeeeddeD~~~~e~e~e~~~~~e 177 (363)
+.+.|+-+.+.+++.++.++.++...+++.++.++.+++++.+.+.+.++..+
T Consensus 209 ~~e~E~v~~D~e~e~~e~~D~E~~~~~~~~~~~~~s~~d~d~e~esd~de~Ee 261 (303)
T KOG3064|consen 209 DAELEEVEGDGELEAEETDDSEDWDGDDDSDESDDSDEDSDSEDESDSDEIEE 261 (303)
T ss_pred hhhhhhccCCcccccccccchhhhcccchhhhhhhcccccccccCCchhhHHH
No 330
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=20.86 E-value=40 Score=32.17 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=20.8
Q ss_pred CCCCcccHhhHH------HHHhc----CCCCCCcCcCCCCC
Q 017955 301 PCGHVYHGDCIV------PWLDS----RNTCPVCRFELPTD 331 (363)
Q Consensus 301 PC~H~Fh~~CI~------~WLk~----~~sCPlCR~~l~~~ 331 (363)
-|+++||.+=.. +|+-+ ..+||+|-++++..
T Consensus 28 ~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~ 68 (250)
T KOG3183|consen 28 GCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTK 68 (250)
T ss_pred CccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCC
Confidence 388888864111 34433 34899999999876
No 331
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.85 E-value=31 Score=33.92 Aligned_cols=31 Identities=16% Similarity=0.330 Sum_probs=22.2
Q ss_pred CceeeeecCCcceeeeccCCCceecccCCCCc
Q 017955 22 TQYWCHHCEKRVSIETLANLPDVICHECKNGF 53 (363)
Q Consensus 22 ~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gF 53 (363)
.-..|-.|...+....+..- -++||.|+..|
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~-~~vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEAN-LNVCPKCGHHM 56 (292)
T ss_pred CeeECCCccchhhHHHHHhc-CCCCCCCCCCe
Confidence 34569999977777643322 27999999877
No 332
>PRK05978 hypothetical protein; Provisional
Probab=20.84 E-value=50 Score=29.28 Aligned_cols=20 Identities=15% Similarity=0.531 Sum_probs=16.9
Q ss_pred HHHhcCCCCCCcCcCCCCCC
Q 017955 313 PWLDSRNTCPVCRFELPTDD 332 (363)
Q Consensus 313 ~WLk~~~sCPlCR~~l~~~d 332 (363)
.+||.+..||.|-..+...+
T Consensus 47 g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 47 AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cccccCCCccccCCccccCC
Confidence 78999999999998886554
No 333
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.66 E-value=48 Score=27.08 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=19.3
Q ss_pred eeeecCCcceeeeccCCCceecccCCCCceee
Q 017955 25 WCHHCEKRVSIETLANLPDVICHECKNGFVES 56 (363)
Q Consensus 25 ~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~ 56 (363)
-|-.|.--|.- +..-.---||.|+|-.||+
T Consensus 60 ~CkkCGfef~~--~~ik~pSRCP~CKSE~Ie~ 89 (97)
T COG3357 60 RCKKCGFEFRD--DKIKKPSRCPKCKSEWIEE 89 (97)
T ss_pred hhcccCccccc--cccCCcccCCcchhhcccC
Confidence 48899933332 1122334699999999875
No 334
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.39 E-value=80 Score=27.32 Aligned_cols=35 Identities=20% Similarity=0.434 Sum_probs=21.9
Q ss_pred CCceeeeecCCcceeeec-cCCCceecccCCCCcee
Q 017955 21 PTQYWCHHCEKRVSIETL-ANLPDVICHECKNGFVE 55 (363)
Q Consensus 21 ~~~~~C~~C~~~~~~~~~-~~~~~~~c~~C~~gFve 55 (363)
.-.|-|..|....-.-.- .+..-+.|-.|++.|+.
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred eEEEECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence 456778778754432211 11245999999998873
No 335
>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=20.30 E-value=43 Score=23.28 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=7.9
Q ss_pred eecccCCCC
Q 017955 44 VICHECKNG 52 (363)
Q Consensus 44 ~~c~~C~~g 52 (363)
++||+|++-
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 789999985
No 336
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.28 E-value=30 Score=31.50 Aligned_cols=36 Identities=22% Similarity=0.513 Sum_probs=24.5
Q ss_pred CCCCceeeeecCCcceeeeccCCCceecccCCCCcee
Q 017955 19 TDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVE 55 (363)
Q Consensus 19 ~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve 55 (363)
+...-|.|-.|..+++..-- ..-.++||.|++--++
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA-~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEA-MELGFTCPKCGEDLEE 144 (176)
T ss_pred ccCCceeCCCCCCcccHHHH-HHhCCCCCCCCchhhh
Confidence 34567999999966665422 2345999999986544
No 337
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.16 E-value=42 Score=24.47 Aligned_cols=14 Identities=21% Similarity=0.404 Sum_probs=9.0
Q ss_pred eecccCCCCceeec
Q 017955 44 VICHECKNGFVESI 57 (363)
Q Consensus 44 ~~c~~C~~gFve~~ 57 (363)
+.||+|+..|-=.|
T Consensus 1 i~CPyCge~~~~~i 14 (52)
T PF14255_consen 1 IQCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCCeeEEEE
Confidence 46888887664443
No 338
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=20.15 E-value=52 Score=35.28 Aligned_cols=37 Identities=27% Similarity=0.643 Sum_probs=25.3
Q ss_pred ccccccccccccccc---CC-------ceEEeCCCCcccHhhHHHHH
Q 017955 279 QETIVCAICKDTVNV---GE-------TATKLPCGHVYHGDCIVPWL 315 (363)
Q Consensus 279 ~~~~~C~ICle~f~~---~e-------~~~~LPC~H~Fh~~CI~~WL 315 (363)
.....|+||.+.|.. ++ ..+.+.=|-+||..|+..-.
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 345679999998863 11 13334358899999997754
No 339
>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=20.12 E-value=56 Score=25.51 Aligned_cols=32 Identities=22% Similarity=0.646 Sum_probs=15.0
Q ss_pred eeeeecCCcceeeeccCCCceecccCCCCceeeccCC
Q 017955 24 YWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVT 60 (363)
Q Consensus 24 ~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~ 60 (363)
++||-|- .+-.+..-.-||.|++.=+..++.-
T Consensus 10 lrC~aCf-----~~t~~~~k~FCp~CGn~TL~rvsvs 41 (73)
T PF08772_consen 10 LRCHACF-----KITKDMTKQFCPKCGNATLKRVSVS 41 (73)
T ss_dssp EE-SSS-------EES-SS--S-SSS--S--EEEE-B
T ss_pred EEccccc-----cCcCCCCceeCcccCCCcceEEEEE
Confidence 5799998 3344556678999999988888754
Done!