Query 014105
Match_columns 430
No_of_seqs 407 out of 1693
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 01:54:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014105.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014105hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 8.1E-57 1.8E-61 460.3 22.6 344 69-429 2-348 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 2.4E-37 5.3E-42 308.6 9.6 227 140-398 145-377 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 9.5E-36 2.1E-40 285.8 10.3 196 138-337 181-405 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 5.7E-26 1.2E-30 210.9 8.9 195 137-338 217-437 (446)
5 smart00647 IBR In Between Ring 99.3 1.9E-12 4E-17 96.8 6.1 63 213-275 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 1.6E-12 3.4E-17 97.1 -0.1 63 213-275 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.7 7.2E-09 1.6E-13 70.4 2.9 40 144-190 1-40 (42)
8 KOG0320 Predicted E3 ubiquitin 98.4 1.4E-07 3.1E-12 82.3 3.3 56 137-203 127-182 (187)
9 PF13923 zf-C3HC4_2: Zinc fing 98.4 2.2E-07 4.7E-12 62.1 2.8 31 144-176 1-32 (39)
10 PF13639 zf-RING_2: Ring finge 98.4 2.1E-07 4.6E-12 63.9 2.4 34 143-176 2-36 (44)
11 PF00097 zf-C3HC4: Zinc finger 98.4 3.8E-07 8.2E-12 61.6 3.4 38 144-190 1-39 (41)
12 PF13445 zf-RING_UBOX: RING-ty 98.3 4.5E-07 9.8E-12 61.6 2.9 41 144-190 1-43 (43)
13 PLN03208 E3 ubiquitin-protein 98.3 5E-07 1.1E-11 81.0 3.8 66 139-208 16-88 (193)
14 smart00647 IBR In Between Ring 98.3 1.5E-06 3.3E-11 64.5 5.1 38 298-336 17-58 (64)
15 PF01485 IBR: IBR domain; Int 98.2 6.6E-07 1.4E-11 66.4 2.0 38 298-336 17-58 (64)
16 PF14634 zf-RING_5: zinc-RING 98.1 2.8E-06 6E-11 58.3 3.0 42 143-195 1-43 (44)
17 PF13920 zf-C3HC4_3: Zinc fing 98.1 3.2E-06 7E-11 59.7 3.1 46 141-199 2-48 (50)
18 cd00162 RING RING-finger (Real 98.0 5.5E-06 1.2E-10 56.3 3.7 44 143-197 1-44 (45)
19 KOG0823 Predicted E3 ubiquitin 98.0 2.7E-06 5.8E-11 77.8 2.7 60 138-207 44-103 (230)
20 KOG0317 Predicted E3 ubiquitin 97.9 8.5E-06 1.9E-10 76.7 3.9 53 138-203 236-288 (293)
21 KOG2177 Predicted E3 ubiquitin 97.9 6.8E-06 1.5E-10 79.8 2.5 109 139-276 11-123 (386)
22 smart00504 Ubox Modified RING 97.8 2.1E-05 4.5E-10 58.2 4.0 48 142-202 2-49 (63)
23 smart00184 RING Ring finger. E 97.8 2.3E-05 5.1E-10 51.2 3.0 30 144-175 1-30 (39)
24 KOG2164 Predicted E3 ubiquitin 97.8 1.1E-05 2.4E-10 81.5 1.9 58 141-206 186-243 (513)
25 PHA02929 N1R/p28-like protein; 97.7 2.6E-05 5.5E-10 73.1 3.8 50 139-199 172-227 (238)
26 PHA02926 zinc finger-like prot 97.7 2.7E-05 5.9E-10 70.7 3.6 56 139-199 168-230 (242)
27 TIGR00599 rad18 DNA repair pro 97.7 2.7E-05 5.9E-10 78.1 3.6 65 139-216 24-89 (397)
28 KOG0287 Postreplication repair 97.5 9.1E-05 2E-09 71.0 3.8 62 141-215 23-85 (442)
29 KOG4367 Predicted Zn-finger pr 97.3 0.00013 2.8E-09 72.0 2.8 34 140-175 3-36 (699)
30 KOG0978 E3 ubiquitin ligase in 97.3 8.8E-05 1.9E-09 78.6 0.9 55 140-206 642-696 (698)
31 TIGR00570 cdk7 CDK-activating 97.0 0.0011 2.4E-08 64.1 5.9 51 142-203 4-58 (309)
32 PF11789 zf-Nse: Zinc-finger o 96.8 0.00091 2E-08 48.4 2.7 47 140-195 10-57 (57)
33 COG5574 PEX10 RING-finger-cont 96.8 0.00097 2.1E-08 62.3 3.5 54 139-203 213-266 (271)
34 PF04564 U-box: U-box domain; 96.8 0.0023 5E-08 48.9 4.7 50 140-201 3-52 (73)
35 COG5540 RING-finger-containing 96.8 0.00091 2E-08 63.4 2.9 51 140-200 322-373 (374)
36 KOG1002 Nucleotide excision re 96.7 0.00084 1.8E-08 68.0 2.4 57 137-201 532-588 (791)
37 PF14555 UBA_4: UBA-like domai 96.6 0.004 8.6E-08 42.4 4.5 41 80-120 1-41 (43)
38 PF12678 zf-rbx1: RING-H2 zinc 96.6 0.0021 4.5E-08 49.2 3.4 35 142-176 20-65 (73)
39 PF14835 zf-RING_6: zf-RING of 96.5 0.00042 9.1E-09 50.7 -0.9 45 141-200 7-52 (65)
40 KOG4628 Predicted E3 ubiquitin 96.4 0.0027 5.8E-08 62.5 3.9 47 142-198 230-277 (348)
41 KOG1814 Predicted E3 ubiquitin 96.4 0.0039 8.4E-08 61.7 4.6 40 297-337 271-312 (445)
42 COG5432 RAD18 RING-finger-cont 96.3 0.0023 5E-08 60.3 2.6 63 141-216 25-88 (391)
43 COG5243 HRD1 HRD ubiquitin lig 96.2 0.016 3.6E-07 56.5 7.6 93 96-199 239-345 (491)
44 PF11793 FANCL_C: FANCL C-term 95.8 0.0045 9.6E-08 46.9 1.6 58 141-200 2-67 (70)
45 PF14570 zf-RING_4: RING/Ubox 95.7 0.0074 1.6E-07 41.8 2.1 45 144-198 1-47 (48)
46 KOG2879 Predicted E3 ubiquitin 95.4 0.017 3.8E-07 54.3 4.0 52 138-199 236-287 (298)
47 KOG0824 Predicted E3 ubiquitin 95.4 0.0083 1.8E-07 57.2 1.8 54 139-204 5-58 (324)
48 COG5152 Uncharacterized conser 95.2 0.0072 1.6E-07 54.0 0.8 34 140-175 195-228 (259)
49 KOG4159 Predicted E3 ubiquitin 95.2 0.024 5.2E-07 57.2 4.6 49 139-200 82-130 (398)
50 KOG0804 Cytoplasmic Zn-finger 95.0 0.14 3.1E-06 51.4 9.4 116 70-199 86-222 (493)
51 KOG1039 Predicted E3 ubiquitin 94.5 0.027 5.8E-07 55.8 3.0 59 136-198 156-220 (344)
52 KOG2660 Locus-specific chromos 94.5 0.015 3.3E-07 56.1 1.2 48 140-199 14-61 (331)
53 KOG0006 E3 ubiquitin-protein l 94.1 0.077 1.7E-06 50.9 4.8 95 160-272 341-438 (446)
54 KOG1734 Predicted RING-contain 93.8 0.043 9.2E-07 51.5 2.5 72 121-201 204-283 (328)
55 KOG0311 Predicted E3 ubiquitin 93.7 0.01 2.2E-07 57.8 -1.7 48 140-198 42-89 (381)
56 PF10571 UPF0547: Uncharacteri 93.6 0.034 7.4E-07 33.4 1.1 24 300-328 1-24 (26)
57 KOG1645 RING-finger-containing 93.6 0.098 2.1E-06 52.0 4.8 49 141-198 4-55 (463)
58 PF12861 zf-Apc11: Anaphase-pr 93.6 0.076 1.6E-06 41.5 3.3 34 157-198 48-81 (85)
59 KOG0802 E3 ubiquitin ligase [P 93.0 0.047 1E-06 58.1 1.7 46 141-197 291-339 (543)
60 KOG0826 Predicted E3 ubiquitin 92.3 0.45 9.7E-06 46.2 7.0 49 140-198 299-347 (357)
61 PF06524 NOA36: NOA36 protein; 91.9 0.18 3.9E-06 47.2 3.8 6 20-25 259-264 (314)
62 KOG4265 Predicted E3 ubiquitin 91.9 0.16 3.4E-06 49.9 3.6 64 124-200 270-337 (349)
63 KOG1428 Inhibitor of type V ad 91.0 0.42 9.2E-06 54.4 6.1 73 141-217 3486-3561(3738)
64 smart00744 RINGv The RING-vari 91.0 0.26 5.7E-06 34.4 3.0 36 143-178 1-41 (49)
65 smart00661 RPOL9 RNA polymeras 90.8 0.19 4E-06 35.4 2.2 27 300-327 1-29 (52)
66 PF05883 Baculo_RING: Baculovi 90.4 0.13 2.9E-06 43.6 1.3 34 141-174 26-66 (134)
67 KOG4692 Predicted E3 ubiquitin 90.3 0.21 4.5E-06 48.7 2.6 53 135-200 416-468 (489)
68 KOG2817 Predicted E3 ubiquitin 90.1 1.5 3.2E-05 43.8 8.4 56 140-203 333-389 (394)
69 KOG4739 Uncharacterized protei 90.0 0.11 2.3E-06 48.5 0.5 46 142-200 4-49 (233)
70 KOG1812 Predicted E3 ubiquitin 89.9 0.4 8.6E-06 48.7 4.5 42 228-273 304-345 (384)
71 PF13240 zinc_ribbon_2: zinc-r 89.8 0.17 3.7E-06 29.4 1.0 10 301-310 1-10 (23)
72 KOG4185 Predicted E3 ubiquitin 89.7 0.51 1.1E-05 46.0 5.0 56 141-206 3-64 (296)
73 KOG0828 Predicted E3 ubiquitin 89.4 0.2 4.2E-06 51.0 1.8 51 140-200 570-635 (636)
74 PF13248 zf-ribbon_3: zinc-rib 88.8 0.23 5.1E-06 29.7 1.2 11 300-310 3-13 (26)
75 KOG1813 Predicted E3 ubiquitin 88.8 0.15 3.2E-06 48.7 0.4 45 141-198 241-285 (313)
76 PHA00626 hypothetical protein 88.4 0.36 7.9E-06 34.2 2.1 28 301-329 2-34 (59)
77 PRK14559 putative protein seri 88.4 0.32 6.9E-06 52.5 2.7 11 325-335 40-50 (645)
78 PF15227 zf-C3HC4_4: zinc fing 88.3 0.2 4.4E-06 33.7 0.7 32 302-340 1-32 (42)
79 KOG0317 Predicted E3 ubiquitin 87.9 0.11 2.3E-06 49.6 -1.2 36 298-340 238-273 (293)
80 COG5220 TFB3 Cdk activating ki 87.3 0.31 6.7E-06 45.1 1.5 49 142-198 11-63 (314)
81 PF09297 zf-NADH-PPase: NADH p 87.2 0.79 1.7E-05 28.8 2.9 29 298-327 2-30 (32)
82 KOG1785 Tyrosine kinase negati 87.1 0.23 5E-06 49.2 0.7 34 141-176 369-402 (563)
83 KOG0297 TNF receptor-associate 87.1 0.56 1.2E-05 47.7 3.5 37 138-176 18-55 (391)
84 PF08274 PhnA_Zn_Ribbon: PhnA 87.0 0.52 1.1E-05 29.3 1.9 27 300-328 3-29 (30)
85 KOG2807 RNA polymerase II tran 86.8 0.2 4.4E-06 48.3 0.1 37 229-272 329-366 (378)
86 KOG1001 Helicase-like transcri 86.5 0.27 5.9E-06 53.3 0.9 50 142-203 455-504 (674)
87 PRK00432 30S ribosomal protein 85.4 0.35 7.6E-06 33.9 0.7 28 298-328 19-47 (50)
88 KOG4172 Predicted E3 ubiquitin 85.1 0.29 6.3E-06 34.6 0.2 45 142-198 8-53 (62)
89 PHA03096 p28-like protein; Pro 84.7 0.47 1E-05 45.9 1.4 38 142-179 179-222 (284)
90 KOG0823 Predicted E3 ubiquitin 84.6 0.42 9.1E-06 44.2 1.0 20 318-340 62-81 (230)
91 PF14835 zf-RING_6: zf-RING of 84.4 0.58 1.3E-05 34.4 1.5 25 300-325 8-35 (65)
92 PF07191 zinc-ribbons_6: zinc- 84.3 0.5 1.1E-05 35.5 1.1 50 301-353 3-57 (70)
93 TIGR00622 ssl1 transcription f 84.0 0.91 2E-05 37.4 2.6 40 231-272 56-102 (112)
94 KOG0827 Predicted E3 ubiquitin 83.9 0.45 9.7E-06 47.1 0.9 50 141-198 4-55 (465)
95 PF10367 Vps39_2: Vacuolar sor 83.5 1 2.2E-05 36.6 2.8 31 141-171 78-108 (109)
96 TIGR00570 cdk7 CDK-activating 83.2 0.74 1.6E-05 44.9 2.1 53 232-313 5-57 (309)
97 PF13923 zf-C3HC4_2: Zinc fing 82.0 0.46 1E-05 31.2 0.1 32 302-339 1-32 (39)
98 KOG1941 Acetylcholine receptor 81.6 2.3 5.1E-05 42.3 4.8 47 141-196 365-413 (518)
99 KOG4275 Predicted E3 ubiquitin 81.6 1.1 2.3E-05 42.9 2.4 28 141-170 300-328 (350)
100 PRK00398 rpoP DNA-directed RNA 81.4 1.3 2.8E-05 30.3 2.2 29 300-329 4-32 (46)
101 PF14952 zf-tcix: Putative tre 81.2 1.3 2.7E-05 29.9 2.0 32 293-328 5-37 (44)
102 PF04931 DNA_pol_phi: DNA poly 80.7 3 6.5E-05 46.5 6.0 20 96-115 764-783 (784)
103 TIGR02098 MJ0042_CXXC MJ0042 f 80.5 0.97 2.1E-05 29.5 1.3 27 300-328 3-35 (38)
104 PF13719 zinc_ribbon_5: zinc-r 80.4 1.5 3.3E-05 28.6 2.2 29 231-261 3-35 (37)
105 KOG1815 Predicted E3 ubiquitin 80.2 1.1 2.3E-05 46.6 2.1 37 299-337 158-197 (444)
106 COG5222 Uncharacterized conser 80.1 1.5 3.4E-05 41.9 3.0 43 142-196 275-318 (427)
107 PF02150 RNA_POL_M_15KD: RNA p 79.4 1.6 3.5E-05 28.1 2.0 28 300-328 2-30 (35)
108 KOG3039 Uncharacterized conser 79.0 1.4 3E-05 41.2 2.2 53 140-203 220-274 (303)
109 PF14803 Nudix_N_2: Nudix N-te 78.6 1.8 3.9E-05 27.8 2.0 27 300-327 1-31 (34)
110 COG5219 Uncharacterized conser 78.6 0.64 1.4E-05 51.0 -0.1 52 139-199 1467-1523(1525)
111 KOG4445 Uncharacterized conser 78.5 1.3 2.7E-05 42.6 1.8 40 139-178 113-153 (368)
112 KOG0320 Predicted E3 ubiquitin 78.3 1 2.2E-05 40.1 1.1 32 253-310 147-178 (187)
113 PRK14559 putative protein seri 78.2 1.9 4E-05 46.7 3.3 9 231-241 2-10 (645)
114 KOG0978 E3 ubiquitin ligase in 77.6 0.98 2.1E-05 48.7 1.0 46 229-309 642-688 (698)
115 KOG3579 Predicted E3 ubiquitin 77.6 1.8 3.9E-05 41.2 2.6 54 139-196 266-322 (352)
116 PF06677 Auto_anti-p27: Sjogre 76.9 5.2 0.00011 26.8 3.9 23 300-325 18-41 (41)
117 PLN03208 E3 ubiquitin-protein 76.9 0.89 1.9E-05 41.2 0.4 31 300-337 19-49 (193)
118 KOG3002 Zn finger protein [Gen 76.7 3.5 7.6E-05 40.3 4.4 77 138-245 45-123 (299)
119 KOG1493 Anaphase-promoting com 76.5 0.72 1.6E-05 35.0 -0.3 48 143-198 22-80 (84)
120 PF09538 FYDLN_acid: Protein o 76.0 1.6 3.5E-05 35.9 1.6 27 300-328 10-36 (108)
121 PLN03086 PRLI-interacting fact 75.3 4.9 0.00011 42.7 5.3 56 186-261 407-463 (567)
122 PRK00420 hypothetical protein; 75.2 5.1 0.00011 33.2 4.3 28 298-335 22-49 (112)
123 KOG2038 CAATT-binding transcri 74.8 2.2 4.8E-05 46.1 2.6 10 5-14 884-893 (988)
124 KOG2906 RNA polymerase III sub 74.6 2.2 4.7E-05 34.0 1.9 30 300-330 2-33 (105)
125 PF02150 RNA_POL_M_15KD: RNA p 74.6 3.1 6.7E-05 26.8 2.3 27 231-260 2-29 (35)
126 PF04641 Rtf2: Rtf2 RING-finge 74.5 4 8.6E-05 39.1 4.2 59 138-208 110-170 (260)
127 KOG3800 Predicted E3 ubiquitin 74.1 4.7 0.0001 38.7 4.3 49 143-201 2-53 (300)
128 PF12773 DZR: Double zinc ribb 73.4 2.7 5.8E-05 29.1 2.0 11 300-310 30-40 (50)
129 TIGR03655 anti_R_Lar restricti 73.2 3 6.5E-05 29.5 2.2 28 300-328 2-36 (53)
130 PF07282 OrfB_Zn_ribbon: Putat 72.9 2.7 5.8E-05 31.3 2.0 29 298-327 27-55 (69)
131 PF04931 DNA_pol_phi: DNA poly 72.8 4.6 9.9E-05 45.1 4.7 6 87-92 709-714 (784)
132 KOG2114 Vacuolar assembly/sort 72.2 5.2 0.00011 43.8 4.6 41 142-197 841-881 (933)
133 PF00627 UBA: UBA/TS-N domain; 72.1 11 0.00024 24.2 4.6 32 81-113 4-35 (37)
134 KOG3970 Predicted E3 ubiquitin 70.9 4.8 0.0001 37.1 3.5 54 142-198 51-104 (299)
135 PF13717 zinc_ribbon_4: zinc-r 70.7 4.1 9E-05 26.4 2.3 29 231-261 3-35 (36)
136 COG5151 SSL1 RNA polymerase II 70.6 0.82 1.8E-05 44.0 -1.5 42 227-270 359-407 (421)
137 COG1998 RPS31 Ribosomal protei 70.2 3.1 6.7E-05 28.8 1.6 26 300-326 20-45 (51)
138 COG5175 MOT2 Transcriptional r 68.8 2.4 5.1E-05 41.4 1.1 53 141-203 14-68 (480)
139 PF14447 Prok-RING_4: Prokaryo 67.8 2.1 4.6E-05 30.5 0.4 44 142-200 8-51 (55)
140 KOG3039 Uncharacterized conser 67.7 4 8.6E-05 38.2 2.3 38 141-180 43-80 (303)
141 KOG0825 PHD Zn-finger protein 67.3 1.9 4.2E-05 46.5 0.3 16 160-175 143-158 (1134)
142 TIGR01384 TFS_arch transcripti 67.1 3.7 7.9E-05 33.4 1.8 25 300-327 1-25 (104)
143 COG1997 RPL43A Ribosomal prote 66.6 4.8 0.0001 31.5 2.2 28 300-328 36-63 (89)
144 PRK08665 ribonucleotide-diphos 66.6 3.6 7.8E-05 45.6 2.2 27 300-329 725-751 (752)
145 cd00194 UBA Ubiquitin Associat 66.0 19 0.00041 23.1 4.8 34 82-116 4-37 (38)
146 KOG2034 Vacuolar sorting prote 65.5 4.4 9.6E-05 44.6 2.5 39 140-178 816-854 (911)
147 KOG3161 Predicted E3 ubiquitin 65.3 2 4.3E-05 45.4 -0.1 36 141-176 11-48 (861)
148 COG5236 Uncharacterized conser 64.0 5.5 0.00012 39.1 2.6 50 137-197 57-106 (493)
149 smart00661 RPOL9 RNA polymeras 63.9 5.9 0.00013 27.5 2.2 27 232-260 2-29 (52)
150 PHA02926 zinc finger-like prot 63.8 3.8 8.3E-05 37.9 1.4 54 298-351 169-224 (242)
151 PF05290 Baculo_IE-1: Baculovi 63.7 6.5 0.00014 33.4 2.6 52 139-198 78-131 (140)
152 PF07975 C1_4: TFIIH C1-like d 63.4 3.1 6.8E-05 29.3 0.6 23 251-273 20-43 (51)
153 COG1645 Uncharacterized Zn-fin 63.0 5.2 0.00011 34.0 2.0 24 299-333 28-51 (131)
154 PHA02929 N1R/p28-like protein; 62.6 3.5 7.5E-05 38.9 1.0 53 230-310 174-227 (238)
155 PRK09710 lar restriction allev 62.5 7.2 0.00016 28.7 2.4 28 298-326 5-35 (64)
156 COG5574 PEX10 RING-finger-cont 61.8 2.3 5E-05 40.2 -0.3 34 300-340 216-250 (271)
157 PF03119 DNA_ligase_ZBD: NAD-d 60.5 8.6 0.00019 23.4 2.1 21 301-321 1-21 (28)
158 KOG1952 Transcription factor N 60.4 6.6 0.00014 43.0 2.7 54 139-196 189-244 (950)
159 PRK05654 acetyl-CoA carboxylas 60.0 2.1 4.6E-05 41.7 -1.0 28 300-328 28-56 (292)
160 PF14446 Prok-RING_1: Prokaryo 59.5 9.3 0.0002 27.2 2.4 32 141-172 5-38 (54)
161 PF10446 DUF2457: Protein of u 59.2 11 0.00024 38.4 3.9 16 136-151 189-204 (458)
162 PF00643 zf-B_box: B-box zinc 58.9 7.6 0.00016 25.6 1.9 31 300-340 4-35 (42)
163 smart00804 TAP_C C-terminal do 58.9 33 0.00071 25.3 5.4 41 76-116 9-49 (63)
164 PF03943 TAP_C: TAP C-terminal 58.6 11 0.00024 26.4 2.7 36 81-116 2-37 (51)
165 PF01599 Ribosomal_S27: Riboso 58.5 7 0.00015 27.0 1.6 27 299-326 18-46 (47)
166 KOG1940 Zn-finger protein [Gen 57.8 7.5 0.00016 37.4 2.3 47 139-196 156-204 (276)
167 COG1594 RPB9 DNA-directed RNA 56.8 8.9 0.00019 31.8 2.4 28 300-328 3-32 (113)
168 smart00165 UBA Ubiquitin assoc 56.4 32 0.00069 21.8 4.5 31 83-114 5-35 (37)
169 TIGR02300 FYDLN_acid conserved 56.2 7 0.00015 32.9 1.6 27 300-328 10-36 (129)
170 COG0266 Nei Formamidopyrimidin 55.9 8.7 0.00019 37.0 2.4 26 299-325 245-272 (273)
171 PF10446 DUF2457: Protein of u 55.5 11 0.00024 38.4 3.2 9 364-372 395-403 (458)
172 PF02891 zf-MIZ: MIZ/SP-RING z 55.1 11 0.00024 26.3 2.2 47 142-196 3-49 (50)
173 PRK14892 putative transcriptio 54.5 9.9 0.00021 30.8 2.2 28 299-327 21-51 (99)
174 KOG1571 Predicted E3 ubiquitin 54.3 7.2 0.00016 38.6 1.6 44 139-198 303-346 (355)
175 CHL00174 accD acetyl-CoA carbo 53.9 2.9 6.2E-05 40.7 -1.2 28 300-328 39-67 (296)
176 PF06827 zf-FPG_IleRS: Zinc fi 53.7 8.8 0.00019 23.5 1.4 25 300-325 2-28 (30)
177 PRK04023 DNA polymerase II lar 53.6 10 0.00022 42.6 2.8 32 227-268 623-660 (1121)
178 PF14445 Prok-RING_2: Prokaryo 53.3 2.7 6E-05 29.2 -1.0 33 140-172 6-39 (57)
179 PRK14714 DNA polymerase II lar 53.1 13 0.00028 42.9 3.5 29 230-268 667-701 (1337)
180 PF14569 zf-UDP: Zinc-binding 53.0 11 0.00023 28.9 2.0 59 231-317 10-69 (80)
181 TIGR00686 phnA alkylphosphonat 52.7 11 0.00023 30.9 2.1 27 300-328 3-29 (109)
182 COG3809 Uncharacterized protei 52.7 47 0.001 25.5 5.4 35 300-341 2-36 (88)
183 KOG2906 RNA polymerase III sub 52.4 14 0.0003 29.6 2.6 27 231-259 2-29 (105)
184 TIGR00515 accD acetyl-CoA carb 52.3 3.3 7.2E-05 40.2 -1.1 28 300-328 27-55 (285)
185 KOG2177 Predicted E3 ubiquitin 52.0 61 0.0013 30.6 7.8 17 316-333 96-112 (386)
186 PF12906 RINGv: RING-variant d 51.8 12 0.00026 25.7 2.0 33 144-176 1-38 (47)
187 PF07800 DUF1644: Protein of u 51.6 23 0.0005 31.1 4.1 84 141-243 2-120 (162)
188 PF13834 DUF4193: Domain of un 51.5 6.2 0.00013 31.7 0.6 32 138-169 67-98 (99)
189 PF06906 DUF1272: Protein of u 51.0 13 0.00029 26.5 2.1 43 143-198 7-51 (57)
190 PF08792 A2L_zn_ribbon: A2L zi 50.9 15 0.00033 23.3 2.2 28 299-327 3-30 (33)
191 PRK11827 hypothetical protein; 50.7 14 0.0003 27.0 2.2 27 300-327 9-35 (60)
192 PF09723 Zn-ribbon_8: Zinc rib 50.5 20 0.00043 24.0 2.9 12 300-311 27-39 (42)
193 PF14569 zf-UDP: Zinc-binding 50.3 24 0.00051 27.1 3.5 50 139-198 7-61 (80)
194 PF08271 TF_Zn_Ribbon: TFIIB z 49.7 19 0.00041 24.1 2.7 24 301-325 2-26 (43)
195 COG5109 Uncharacterized conser 49.6 19 0.00041 35.0 3.6 51 140-198 335-386 (396)
196 PF05715 zf-piccolo: Piccolo Z 49.6 7.2 0.00016 28.2 0.6 40 300-340 3-44 (61)
197 PF08746 zf-RING-like: RING-li 49.5 16 0.00034 24.7 2.2 34 144-177 1-35 (43)
198 KOG2038 CAATT-binding transcri 49.0 11 0.00025 40.9 2.2 7 3-9 874-880 (988)
199 PF04147 Nop14: Nop14-like fam 48.9 54 0.0012 37.0 7.6 17 64-80 417-436 (840)
200 PF01363 FYVE: FYVE zinc finge 48.5 15 0.00032 27.2 2.2 35 299-336 9-43 (69)
201 PRK14811 formamidopyrimidine-D 48.3 14 0.0003 35.6 2.6 27 299-326 235-263 (269)
202 PF13453 zf-TFIIB: Transcripti 48.0 12 0.00027 24.7 1.5 32 301-339 1-32 (41)
203 PRK12286 rpmF 50S ribosomal pr 46.7 13 0.00027 26.9 1.5 23 298-326 26-48 (57)
204 PF09788 Tmemb_55A: Transmembr 46.6 20 0.00043 33.9 3.2 20 228-247 121-140 (256)
205 COG1198 PriA Primosomal protei 46.2 17 0.00036 40.1 3.0 36 299-335 444-484 (730)
206 PF09889 DUF2116: Uncharacteri 45.0 4.5 9.8E-05 29.4 -1.0 11 300-310 4-14 (59)
207 PF14149 YhfH: YhfH-like prote 45.0 1.7 3.7E-05 28.3 -2.8 25 299-324 13-37 (37)
208 PRK01103 formamidopyrimidine/5 44.8 17 0.00036 35.1 2.5 26 299-325 245-272 (274)
209 COG0777 AccD Acetyl-CoA carbox 44.5 7 0.00015 37.4 -0.1 29 300-329 29-58 (294)
210 cd00021 BBOX B-Box-type zinc f 44.3 18 0.00038 23.1 1.9 26 301-334 2-28 (39)
211 TIGR00577 fpg formamidopyrimid 44.1 18 0.00038 35.0 2.6 26 299-325 245-272 (272)
212 PRK10220 hypothetical protein; 44.1 18 0.0004 29.6 2.2 27 300-328 4-30 (111)
213 PRK14810 formamidopyrimidine-D 44.0 17 0.00037 35.0 2.5 26 299-325 244-271 (272)
214 PF02845 CUE: CUE domain; Int 43.5 76 0.0016 20.9 4.9 37 81-117 3-40 (42)
215 PRK14714 DNA polymerase II lar 43.4 14 0.00031 42.5 2.0 30 300-336 668-702 (1337)
216 PRK10445 endonuclease VIII; Pr 43.1 18 0.0004 34.6 2.5 25 300-325 236-262 (263)
217 PRK13945 formamidopyrimidine-D 42.7 19 0.0004 35.0 2.5 26 299-325 254-281 (282)
218 COG5432 RAD18 RING-finger-cont 42.5 8 0.00017 37.1 -0.1 29 300-335 26-54 (391)
219 TIGR00599 rad18 DNA repair pro 42.2 8.4 0.00018 39.2 -0.0 32 300-338 27-58 (397)
220 COG2816 NPY1 NTP pyrophosphohy 42.1 25 0.00054 33.9 3.2 37 290-328 103-139 (279)
221 PF00098 zf-CCHC: Zinc knuckle 41.7 17 0.00037 19.6 1.2 16 261-276 2-17 (18)
222 smart00659 RPOLCX RNA polymera 41.7 23 0.00051 24.0 2.1 10 300-309 20-29 (44)
223 PF07754 DUF1610: Domain of un 41.6 21 0.00045 21.0 1.6 7 300-306 17-23 (24)
224 KOG2930 SCF ubiquitin ligase, 41.6 19 0.0004 29.2 1.8 17 160-176 80-96 (114)
225 COG5194 APC11 Component of SCF 41.5 20 0.00043 27.6 1.9 17 160-176 53-69 (88)
226 PF15616 TerY-C: TerY-C metal 41.2 16 0.00035 31.1 1.6 24 299-330 77-100 (131)
227 PF10122 Mu-like_Com: Mu-like 41.1 11 0.00024 26.4 0.5 26 300-326 5-32 (51)
228 KOG1991 Nuclear transport rece 40.9 60 0.0013 36.6 6.2 34 69-105 954-987 (1010)
229 TIGR01031 rpmF_bact ribosomal 40.2 17 0.00037 26.0 1.4 23 298-326 25-47 (55)
230 KOG2932 E3 ubiquitin ligase in 40.1 7.7 0.00017 37.6 -0.6 53 227-316 87-140 (389)
231 KOG4362 Transcriptional regula 40.1 7 0.00015 42.2 -1.0 51 141-201 21-71 (684)
232 PF06844 DUF1244: Protein of u 39.3 20 0.00044 26.5 1.6 17 164-180 11-27 (68)
233 PF01428 zf-AN1: AN1-like Zinc 39.1 20 0.00043 24.1 1.5 28 233-267 1-29 (43)
234 TIGR01053 LSD1 zinc finger dom 38.9 33 0.00072 21.4 2.3 25 301-326 3-27 (31)
235 PRK04023 DNA polymerase II lar 38.9 16 0.00035 41.1 1.5 32 297-335 624-660 (1121)
236 PRK09710 lar restriction allev 38.8 42 0.00092 24.8 3.2 32 229-261 5-37 (64)
237 PF12861 zf-Apc11: Anaphase-pr 38.1 14 0.0003 29.0 0.6 35 300-339 33-67 (85)
238 KOG1991 Nuclear transport rece 37.7 16 0.00035 40.9 1.2 25 75-99 968-993 (1010)
239 PF15135 UPF0515: Uncharacteri 37.2 30 0.00064 32.6 2.7 20 92-111 8-27 (278)
240 PF01783 Ribosomal_L32p: Ribos 37.0 18 0.0004 25.9 1.1 22 298-325 25-46 (56)
241 KOG3053 Uncharacterized conser 37.0 27 0.00059 33.0 2.5 55 140-197 19-80 (293)
242 PF14471 DUF4428: Domain of un 36.8 31 0.00067 24.2 2.2 30 143-173 1-30 (51)
243 PRK00241 nudC NADH pyrophospha 36.6 36 0.00078 32.5 3.4 35 292-328 93-127 (256)
244 PRK12495 hypothetical protein; 36.0 49 0.0011 30.7 3.9 17 299-315 42-58 (226)
245 KOG2141 Protein involved in hi 35.7 29 0.00064 37.6 2.8 20 376-395 666-693 (822)
246 PF05129 Elf1: Transcription e 35.7 19 0.00042 27.9 1.1 29 299-328 22-56 (81)
247 PRK08115 ribonucleotide-diphos 35.7 19 0.00041 40.3 1.4 26 300-328 828-854 (858)
248 PHA02664 hypothetical protein; 35.4 66 0.0014 31.5 4.8 13 78-90 513-525 (534)
249 KOG1701 Focal adhesion adaptor 35.4 18 0.00039 36.7 1.1 11 300-310 428-438 (468)
250 COG1594 RPB9 DNA-directed RNA 35.4 39 0.00085 28.0 3.0 29 230-260 2-31 (113)
251 PF03604 DNA_RNApol_7kD: DNA d 35.4 22 0.00048 22.4 1.1 10 300-309 18-27 (32)
252 PRK09521 exosome complex RNA-b 35.4 27 0.00059 31.6 2.2 27 300-328 150-176 (189)
253 PLN02638 cellulose synthase A 35.3 26 0.00056 40.0 2.4 60 232-319 19-79 (1079)
254 PLN02189 cellulose synthase 35.1 30 0.00064 39.4 2.8 61 231-319 35-96 (1040)
255 smart00834 CxxC_CXXC_SSSS Puta 35.1 23 0.0005 23.0 1.3 12 300-311 27-38 (41)
256 KOG2979 Protein involved in DN 35.0 36 0.00077 32.3 2.9 48 141-196 176-223 (262)
257 KOG3241 Uncharacterized conser 34.7 35 0.00077 30.4 2.7 8 51-58 213-220 (227)
258 PF12760 Zn_Tnp_IS1595: Transp 34.7 62 0.0013 21.9 3.4 28 298-326 17-45 (46)
259 PF02318 FYVE_2: FYVE-type zin 34.6 47 0.001 27.6 3.4 36 298-335 53-88 (118)
260 PF06943 zf-LSD1: LSD1 zinc fi 34.6 43 0.00093 19.9 2.2 24 302-326 1-24 (25)
261 PHA02825 LAP/PHD finger-like p 34.2 42 0.00092 29.5 3.1 49 139-199 6-59 (162)
262 KOG2879 Predicted E3 ubiquitin 33.8 17 0.00036 34.8 0.6 31 299-335 239-269 (298)
263 COG5220 TFB3 Cdk activating ki 33.2 24 0.00052 33.0 1.5 54 187-244 11-65 (314)
264 PF05605 zf-Di19: Drought indu 33.0 21 0.00046 25.1 0.9 45 141-203 2-46 (54)
265 PF01396 zf-C4_Topoisom: Topoi 32.7 46 0.001 21.8 2.4 21 300-321 2-25 (39)
266 COG1096 Predicted RNA-binding 32.5 30 0.00065 31.3 1.9 25 300-327 150-174 (188)
267 KOG4684 Uncharacterized conser 32.2 44 0.00096 30.7 2.9 19 228-246 136-154 (275)
268 KOG2164 Predicted E3 ubiquitin 32.1 17 0.00037 37.7 0.4 30 299-335 186-215 (513)
269 TIGR00595 priA primosomal prot 32.1 37 0.0008 35.9 2.9 35 300-335 223-262 (505)
270 KOG0309 Conserved WD40 repeat- 31.8 33 0.00073 37.4 2.4 37 140-176 1027-1063(1081)
271 smart00336 BBOX B-Box-type zin 31.6 52 0.0011 21.2 2.6 31 300-340 4-35 (42)
272 COG2824 PhnA Uncharacterized Z 31.3 37 0.00079 27.7 2.0 26 300-328 4-30 (112)
273 PLN02436 cellulose synthase A 31.3 41 0.0009 38.4 3.2 50 139-198 34-88 (1094)
274 PF14354 Lar_restr_allev: Rest 30.8 55 0.0012 23.4 2.8 29 229-259 2-37 (61)
275 PF02042 RWP-RK: RWP-RK domain 30.6 77 0.0017 22.4 3.3 37 69-105 4-40 (52)
276 PRK14892 putative transcriptio 30.3 62 0.0013 26.2 3.2 56 226-286 17-74 (99)
277 cd00065 FYVE FYVE domain; Zinc 30.1 31 0.00068 24.2 1.4 34 300-336 3-36 (57)
278 TIGR01206 lysW lysine biosynth 30.0 53 0.0012 23.4 2.5 28 232-261 4-32 (54)
279 COG3024 Uncharacterized protei 30.0 25 0.00055 25.8 0.9 13 299-311 7-19 (65)
280 COG2051 RPS27A Ribosomal prote 29.8 69 0.0015 23.8 3.1 30 231-263 20-50 (67)
281 KOG3268 Predicted E3 ubiquitin 29.8 55 0.0012 29.2 3.0 59 140-200 164-229 (234)
282 COG4640 Predicted membrane pro 29.7 27 0.00059 35.1 1.3 23 300-328 2-25 (465)
283 PF03615 GCM: GCM motif protei 29.6 55 0.0012 27.8 2.9 22 300-327 83-106 (143)
284 PF02724 CDC45: CDC45-like pro 29.4 93 0.002 33.9 5.4 6 193-198 352-357 (622)
285 COG5082 AIR1 Arginine methyltr 29.4 40 0.00087 30.6 2.2 17 259-275 78-94 (190)
286 PHA02325 hypothetical protein 29.0 26 0.00056 25.7 0.7 12 298-309 2-13 (72)
287 PF04050 Upf2: Up-frameshift s 28.8 40 0.00087 30.0 2.2 13 72-84 62-74 (170)
288 PLN02400 cellulose synthase 28.1 54 0.0012 37.6 3.3 60 232-319 38-98 (1085)
289 TIGR02443 conserved hypothetic 27.2 57 0.0012 23.7 2.2 27 300-327 10-40 (59)
290 PF10497 zf-4CXXC_R1: Zinc-fin 26.7 75 0.0016 25.9 3.2 34 162-197 37-70 (105)
291 PF01780 Ribosomal_L37ae: Ribo 26.6 41 0.00089 26.7 1.6 28 300-328 36-63 (90)
292 PLN02915 cellulose synthase A 26.1 51 0.0011 37.6 2.7 56 238-319 21-77 (1044)
293 PF06056 Terminase_5: Putative 26.0 90 0.0019 22.5 3.2 30 82-111 15-44 (58)
294 PRK14873 primosome assembly pr 25.8 49 0.0011 36.2 2.6 34 300-334 393-430 (665)
295 KOG2932 E3 ubiquitin ligase in 25.8 33 0.00072 33.4 1.1 29 299-334 90-119 (389)
296 PLN02189 cellulose synthase 25.8 58 0.0013 37.2 3.1 50 139-198 32-86 (1040)
297 PRK05580 primosome assembly pr 25.5 55 0.0012 36.0 2.9 35 300-335 391-430 (679)
298 COG3813 Uncharacterized protei 25.3 54 0.0012 24.7 1.9 44 143-199 7-52 (84)
299 PLN02436 cellulose synthase A 25.2 57 0.0012 37.3 2.9 60 232-319 38-98 (1094)
300 KOG4739 Uncharacterized protei 25.1 1.8E+02 0.004 27.3 5.8 24 313-337 21-48 (233)
301 TIGR02159 PA_CoA_Oxy4 phenylac 24.7 51 0.0011 28.7 2.0 66 103-172 67-139 (146)
302 PF11781 RRN7: RNA polymerase 24.5 43 0.00094 21.7 1.1 25 299-326 8-33 (36)
303 PF09526 DUF2387: Probable met 24.2 65 0.0014 24.4 2.2 27 300-327 9-39 (71)
304 PF04216 FdhE: Protein involve 24.2 60 0.0013 31.5 2.6 10 230-241 172-181 (290)
305 PLN02638 cellulose synthase A 24.2 74 0.0016 36.5 3.5 50 139-198 15-69 (1079)
306 COG4530 Uncharacterized protei 24.0 85 0.0018 25.7 2.9 11 19-29 77-87 (129)
307 KOG3002 Zn finger protein [Gen 24.0 43 0.00093 32.8 1.5 31 229-267 47-77 (299)
308 PLN03086 PRLI-interacting fact 23.9 44 0.00096 35.7 1.7 30 298-328 432-463 (567)
309 smart00064 FYVE Protein presen 23.7 66 0.0014 23.5 2.2 36 141-176 10-47 (68)
310 COG5243 HRD1 HRD ubiquitin lig 23.7 69 0.0015 32.1 2.8 11 300-310 335-345 (491)
311 PF03833 PolC_DP2: DNA polymer 23.6 27 0.00058 38.8 0.0 32 299-337 655-691 (900)
312 PF05320 Pox_RNA_Pol_19: Poxvi 23.5 28 0.0006 30.3 0.1 9 141-149 126-134 (167)
313 PF14353 CpXC: CpXC protein 23.1 44 0.00096 28.0 1.3 46 187-244 2-50 (128)
314 smart00154 ZnF_AN1 AN1-like Zi 23.0 54 0.0012 21.6 1.4 14 317-331 12-25 (39)
315 PF03854 zf-P11: P-11 zinc fin 23.0 28 0.00062 24.0 0.0 44 142-200 3-47 (50)
316 KOG0825 PHD Zn-finger protein 22.6 62 0.0013 35.6 2.4 41 141-181 96-141 (1134)
317 PRK00415 rps27e 30S ribosomal 22.6 1.1E+02 0.0025 22.2 3.1 29 231-262 12-41 (59)
318 PRK03564 formate dehydrogenase 22.5 99 0.0021 30.5 3.7 39 232-306 189-233 (309)
319 KOG2789 Putative Zn-finger pro 22.4 30 0.00065 34.8 0.1 35 139-173 72-106 (482)
320 TIGR00264 alpha-NAC-related pr 22.4 1.7E+02 0.0037 24.4 4.5 35 78-112 77-111 (116)
321 PF01667 Ribosomal_S27e: Ribos 22.4 1.1E+02 0.0024 21.9 2.9 30 231-263 8-38 (55)
322 PRK06369 nac nascent polypepti 21.9 2.1E+02 0.0045 23.8 4.9 34 79-112 76-109 (115)
323 PF11682 DUF3279: Protein of u 21.7 52 0.0011 27.9 1.4 11 300-310 111-121 (128)
324 PF15387 DUF4611: Domain of un 21.7 78 0.0017 25.2 2.2 14 30-43 61-74 (96)
325 KOG0298 DEAD box-containing he 21.6 31 0.00067 39.9 0.0 39 139-178 1151-1189(1394)
326 PF14369 zf-RING_3: zinc-finge 21.6 93 0.002 19.9 2.2 28 231-261 3-31 (35)
327 PF04216 FdhE: Protein involve 21.4 45 0.00099 32.4 1.2 35 300-335 173-220 (290)
328 KOG2041 WD40 repeat protein [G 21.3 87 0.0019 34.2 3.2 22 206-227 1088-1109(1189)
329 PRK11426 hypothetical protein; 21.0 1.5E+02 0.0032 25.4 4.0 37 68-104 59-96 (132)
330 TIGR00280 L37a ribosomal prote 21.0 60 0.0013 25.8 1.5 29 299-328 35-63 (91)
331 PRK03976 rpl37ae 50S ribosomal 20.9 59 0.0013 25.8 1.4 29 299-328 36-64 (90)
332 KOG2548 SWAP mRNA splicing reg 20.8 2.4E+02 0.0053 29.6 6.1 12 323-334 559-570 (653)
333 PF10426 zf-RAG1: Recombinatio 20.7 34 0.00073 21.2 0.0 18 186-203 2-19 (30)
334 PRK08332 ribonucleotide-diphos 20.7 62 0.0013 39.2 2.2 28 300-330 1705-1738(1740)
335 PLN02915 cellulose synthase A 20.6 99 0.0021 35.4 3.6 52 138-199 12-68 (1044)
336 PLN00209 ribosomal protein S27 20.6 1.1E+02 0.0025 23.9 2.9 30 231-263 37-67 (86)
337 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.5 68 0.0015 28.2 2.0 27 300-328 35-61 (166)
338 PTZ00083 40S ribosomal protein 20.4 1.1E+02 0.0025 23.8 2.9 30 231-263 36-66 (85)
339 PRK14890 putative Zn-ribbon RN 20.1 79 0.0017 23.0 1.8 32 300-332 8-39 (59)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.1e-57 Score=460.32 Aligned_cols=344 Identities=47% Similarity=0.907 Sum_probs=316.2
Q ss_pred EecHHHHHHHHHHHHHHHHhHcCCCHHHHHHHHHhcCCChhhhhhhhhhcHHHHHHHhCCCCCCCcCCCCCCcccccccc
Q 014105 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPDGEEMTCGICF 148 (430)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~C~IC~ 148 (430)
+|+.++|...|.+.|..|+++|++++..|++||.+|.|+..++++.|+.+++.++..+|+...+ ......+|.||+
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~----~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWP----KKKGDVQCGICV 77 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccC----CCCccccCCccc
Confidence 6889999999999999999999999999999999999999999999999999999999987654 345578999999
Q ss_pred ccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcCh-HHHHHHHHHHHHHHHhcC
Q 014105 149 ENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSD-EDKVKYNRYFIRSYVEDN 227 (430)
Q Consensus 149 e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~-e~~~ky~~~~~~~~v~~~ 227 (430)
+.++. .+..+.|||.||..||..|+..+|..+.... |+||...|.+.+..+.|..++++ +...+|.++++++|++.+
T Consensus 78 ~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~-i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~ 155 (444)
T KOG1815|consen 78 ESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK-IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-hhhhcCCCcHHHHHHHHHHhhheeecccccc-ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 98865 6788899999999999999999999986433 99999999999999999999988 499999999999999999
Q ss_pred CCceecCCCCCCceEEeecCCCCceEEecCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCc
Q 014105 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKR 307 (430)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~ 307 (430)
..++|||+|+|+.++.+. ......|.|.|++.|||.|+.+||.|.+|.....|+.+...++++.+||.+|+++||+|.+
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~ 234 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKV 234 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCccc
Confidence 999999999999999875 4456889999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecCCCCceEecCC--CccccccccccccccCCCCCCCcccCCchhhhhccCCCcHHHHHHHHHHhhhhhhhhHHHHH
Q 014105 308 PIEKNQGCMHMTCTPP--CKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVYDESEKRREMAKNSLERYTHYYERW 385 (430)
Q Consensus 308 ~IeK~~GCnhm~C~~~--C~~~FCw~C~~~~~~h~~~~g~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~l~ry~~y~~r~ 385 (430)
+|||++|||||+|. . |++.|||+|++.|.+|+..+ +|.|++|...+.. . .+++++..|.||.|||.||
T Consensus 235 ~iek~~gc~~~~~~-~~~c~~~FCw~Cl~~~~~h~~~~--~~~c~~~~~~~~~------~-~~~~a~~~l~r~~~~~~~~ 304 (444)
T KOG1815|consen 235 PIEKDGGCNHMTCK-SASCKHEFCWVCLASLSDHGSST--GYSCNRYVDGKSK------S-ARSKARRSLKRYTHYYNRW 304 (444)
T ss_pred chhccCCccccccc-cCCcCCeeceeeecccccccccc--eeeeeeeechhhh------h-HHHHHHHHHHHHHHHHhhH
Confidence 99999999999998 6 99999999999999999755 8999999876431 1 5788999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCceeEeecccC
Q 014105 386 ATNQSSRQKALADLQQMQTVHVTKRCTVPTRVTAQVHHRSLATD 429 (430)
Q Consensus 386 ~~~~~s~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 429 (430)
++|+.|++++...+..+......++.....++..++.++.++.+
T Consensus 305 ~~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 (444)
T KOG1815|consen 305 MEHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGD 348 (444)
T ss_pred HhhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHH
Confidence 99999999999999999999999999998899999999988753
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-37 Score=308.62 Aligned_cols=227 Identities=27% Similarity=0.660 Sum_probs=189.5
Q ss_pred CccccccccccccC-CCeee-ccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcChHHHHHHHH
Q 014105 140 EEMTCGICFENYPS-DRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (430)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~-l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~ 217 (430)
...+|.||+...+. ..++. ..|+|.||.+||++|++.+...| ..++||..+|...++......++++++.++|.+
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~---~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG---TVIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC---CCccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 46789999955443 34444 56999999999999999995555 489999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCceecCCCCCCceEEeecC---CCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHH
Q 014105 218 YFIRSYVEDNRKTKWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMN 293 (430)
Q Consensus 218 ~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~ 293 (430)
++.+.++.....+ +||+|+|...+....- .......| .|+..||.+|+.+||.+.+|.++++|......+..+.+
T Consensus 222 ~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~ 300 (384)
T KOG1812|consen 222 RLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLK 300 (384)
T ss_pred HHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHH
Confidence 9999999988888 9999999887654321 22345578 89999999999999999999999999877677777888
Q ss_pred HHHhcCCCCCCCCcceeecCCCCceEecCCCccccccccccccccCCCCCCCcccCCchhhhhccCCCcHHHHHHHHHHh
Q 014105 294 WILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVYDESEKRREMAKN 373 (430)
Q Consensus 294 ~i~~~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~~~C~~~~~~~~~~~~~~~~~~~~~~~~ 373 (430)
|+.++++.||+|+..|++++|||||+|+ ||++|||.|+++|..|+. .+|.|.++...
T Consensus 301 ~la~~wr~CpkC~~~ie~~~GCnhm~Cr--C~~~fcy~C~~~~~~~~~---~~~~~~r~~~~------------------ 357 (384)
T KOG1812|consen 301 YLAKRWRQCPKCKFMIELSEGCNHMTCR--CGHQFCYMCGGDWKTHNG---ECYECCRYKES------------------ 357 (384)
T ss_pred HHHHhcCcCcccceeeeecCCcceEEee--ccccchhhcCcchhhCCc---cccCccccccc------------------
Confidence 8888999999999999999999999998 999999999999998875 45666666422
Q ss_pred hhhhhhhHHHHHhhhHHHHHHHHHH
Q 014105 374 SLERYTHYYERWATNQSSRQKALAD 398 (430)
Q Consensus 374 ~l~ry~~y~~r~~~~~~s~~~~~~~ 398 (430)
+++|.++.++..+.+.....
T Consensus 358 -----~~~~~~~~~~~~~~~~~~~~ 377 (384)
T KOG1812|consen 358 -----THYFEDDENHDKSIQLEAED 377 (384)
T ss_pred -----cccccccccccccccccccc
Confidence 66777787777765554433
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.5e-36 Score=285.77 Aligned_cols=196 Identities=30% Similarity=0.703 Sum_probs=171.3
Q ss_pred CCCccccccccccccC-CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcChHHHHHHH
Q 014105 138 DGEEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYN 216 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~ 216 (430)
....+.|.|||+.... ..++.++|+|+||+.|++.|+...|++|. +..++||+++|+...++..++.++..+++++|+
T Consensus 181 ~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~-v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQ-VSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcce-eeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 3457899999998765 57889999999999999999999999986 678999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCceecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHH--------HHH-----
Q 014105 217 RYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVA--------KWV----- 282 (430)
Q Consensus 217 ~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~--------~~~----- 282 (430)
++++.+.++...++++||++.|..++.. ..+...+.| .|..+||+.|+..||...+|..-. .|.
T Consensus 260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~--d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRACCQLPVKQ--DPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCcccc--CchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 9999999999999999999999998743 345677899 999999999999999999997541 121
Q ss_pred --------------HhhhhhHHHHHHHHhcCCCCCCCCcceeecCCCCceEecCCCccccccccccccc
Q 014105 283 --------------LKNSAESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (430)
Q Consensus 283 --------------~~~~~e~~~~~~i~~~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (430)
.....+..+.+|+..|.|+||+|+++|||++|||||+|. .|++.|||+|.....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~-~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT-KCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec-cccccceeehhhhcC
Confidence 111233445689999999999999999999999999999 899999999998754
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=5.7e-26 Score=210.95 Aligned_cols=195 Identities=31% Similarity=0.695 Sum_probs=150.6
Q ss_pred CCCCccccccccccccCCCeeeccCC--CcccHHHHHHHHHhhhcCCC------ceeecccCCCCCCCCchh-hHHHhhc
Q 014105 137 PDGEEMTCGICFENYPSDRLLAAACG--HPFCSSCWTGYISTAINDGP------GCLMLRCPDPSCGAAVGQ-DMIYLLS 207 (430)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~yi~~~i~~g~------~~~~i~CP~~~C~~~l~~-~~i~~ll 207 (430)
.+....+|..|-+.- +.+..++|. |..|.+|++.|..+.+++.. ....+.||. +|...+-. -.-.+++
T Consensus 217 ~N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 217 TNSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred cccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 356788999998753 445567888 99999999999999997642 124678885 78776533 3345688
Q ss_pred ChHHHHHHHHHHHHHHHhcCCCceecCCCCCCceEEeecCCCCceEEe--cCCCccccccCCcCCCCCCchhHHH-----
Q 014105 208 SDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC--RCSYSFCWNCTEEAHRPVDCDTVAK----- 280 (430)
Q Consensus 208 ~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C--~C~~~fC~~C~~~~H~~~~C~~~~~----- 280 (430)
..+.+.+|+++..+.+|.... -+.||+|+|+..+...+ ....|+| .|++.||.+|++.+|.+. |...-.
T Consensus 294 g~e~Y~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~t~ 369 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASGTT 369 (446)
T ss_pred chhHHHHHHHhhhhhheeecC-CEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhcccc-ceeeecccccc
Confidence 999999999999999988776 57999999998876654 4678999 499999999999999873 431100
Q ss_pred ---H-HHhhhh-----hHHHHHHHHhcCCCCCCCCcceeecCCCCceEecC-CCcccccccccccccc
Q 014105 281 ---W-VLKNSA-----ESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLGQWSD 338 (430)
Q Consensus 281 ---~-~~~~~~-----e~~~~~~i~~~tk~CP~C~~~IeK~~GCnhm~C~~-~C~~~FCw~C~~~~~~ 338 (430)
+ ...+.+ +..+..-|+..||+||+|+++.||||||+||.|+. .||.+|||.|+..|..
T Consensus 370 tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 370 TCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 0 000111 22334458889999999999999999999999983 5999999999999974
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.34 E-value=1.9e-12 Score=96.76 Aligned_cols=63 Identities=46% Similarity=1.028 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHhcCCCceecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCc
Q 014105 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (430)
Q Consensus 213 ~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C 275 (430)
++|.+++++++|+.+++++|||+|+|+.++......+...|.| .|++.||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4789999999999999999999999999988753345678999 99999999999999999987
No 6
>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=99.22 E-value=1.6e-12 Score=97.14 Aligned_cols=63 Identities=35% Similarity=0.964 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHhcCCCceecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCc
Q 014105 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (430)
Q Consensus 213 ~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C 275 (430)
++|.+++++.+++.++.++|||+|+|+.++..........+.| .|++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 4788889999998889999999999999998775443335999 69999999999999999887
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.73 E-value=7.2e-09 Score=70.36 Aligned_cols=40 Identities=30% Similarity=0.848 Sum_probs=30.0
Q ss_pred cccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccC
Q 014105 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (430)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP 190 (430)
|+||++.+ .++++++|||.||..|+..++...-.. .+.||
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~-----~~~CP 40 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGS-----GFSCP 40 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSS-----T---S
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCc-----CCCCc
Confidence 89999988 899999999999999999999764322 37898
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.43 E-value=1.4e-07 Score=82.30 Aligned_cols=56 Identities=23% Similarity=0.685 Sum_probs=45.4
Q ss_pred CCCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
.+...+.||||++.+....+++..|||.||..|++.-+.. ..+|| .|+..|....+
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~---------~~~CP--~C~kkIt~k~~ 182 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN---------TNKCP--TCRKKITHKQF 182 (187)
T ss_pred ccccccCCCceecchhhccccccccchhHHHHHHHHHHHh---------CCCCC--Ccccccchhhh
Confidence 3456789999999998777888999999999999988776 34799 78877765544
No 9
>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=98.39 E-value=2.2e-07 Score=62.10 Aligned_cols=31 Identities=32% Similarity=1.006 Sum_probs=26.5
Q ss_pred cccccccccCCCe-eeccCCCcccHHHHHHHHHh
Q 014105 144 CGICFENYPSDRL-LAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 144 C~IC~e~~~~~~~-~~l~CgH~fC~~Cl~~yi~~ 176 (430)
|+||++.+ .++ +.++|||.||.+||.+|++.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHC
Confidence 89999976 345 68899999999999999887
No 10
>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=98.37 E-value=2.1e-07 Score=63.93 Aligned_cols=34 Identities=29% Similarity=0.885 Sum_probs=30.4
Q ss_pred cccccccccc-CCCeeeccCCCcccHHHHHHHHHh
Q 014105 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~yi~~ 176 (430)
+|+||++.+. ...++.++|||.||.+|+..|+..
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh
Confidence 5999999985 467788899999999999999977
No 11
>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=98.36 E-value=3.8e-07 Score=61.57 Aligned_cols=38 Identities=34% Similarity=1.093 Sum_probs=31.6
Q ss_pred cccccccccCCCee-eccCCCcccHHHHHHHHHhhhcCCCceeecccC
Q 014105 144 CGICFENYPSDRLL-AAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (430)
Q Consensus 144 C~IC~e~~~~~~~~-~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP 190 (430)
|+||++.+ ..+. .++|||.||..||.+++.. .+ .++||
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~---~~----~~~CP 39 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLEN---SG----SVKCP 39 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHH---TS----SSBTT
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHHHh---cC----CccCC
Confidence 89999987 4444 8899999999999999998 22 56798
No 12
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.31 E-value=4.5e-07 Score=61.61 Aligned_cols=41 Identities=29% Similarity=0.812 Sum_probs=23.3
Q ss_pred cccccccccC--CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccC
Q 014105 144 CGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (430)
Q Consensus 144 C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP 190 (430)
|+||.+ +.. +.++.|+|||.||++|+.+.+..... ..++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~-----~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDR-----NRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S------S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCC-----CeeeCc
Confidence 899999 632 34788999999999999999986431 268887
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.30 E-value=5e-07 Score=81.04 Aligned_cols=66 Identities=23% Similarity=0.582 Sum_probs=48.1
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCC-------CceeecccCCCCCCCCchhhHHHhhcC
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDG-------PGCLMLRCPDPSCGAAVGQDMIYLLSS 208 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g-------~~~~~i~CP~~~C~~~l~~~~i~~ll~ 208 (430)
...++|+||++.+ .+++.++|||.||..|+..|+...-... ......+|| .|+..+....+..+..
T Consensus 16 ~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiyg 88 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYG 88 (193)
T ss_pred CCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeec
Confidence 4578999999976 6778889999999999999986421100 001257999 8999997766655443
No 14
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.26 E-value=1.5e-06 Score=64.50 Aligned_cols=38 Identities=39% Similarity=1.046 Sum_probs=34.5
Q ss_pred cCCCCC--CCCcceeecC--CCCceEecCCCcccccccccccc
Q 014105 298 NSKPCP--RCKRPIEKNQ--GCMHMTCTPPCKFEFCWLCLGQW 336 (430)
Q Consensus 298 ~tk~CP--~C~~~IeK~~--GCnhm~C~~~C~~~FCw~C~~~~ 336 (430)
+.+.|| +|+..|+... |..+|+|. .|++.|||.|+.+|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~-~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCP-KCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECC-CCCCeECCCCCCcC
Confidence 468899 9999999964 99999997 69999999999988
No 15
>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=98.20 E-value=6.6e-07 Score=66.45 Aligned_cols=38 Identities=45% Similarity=1.097 Sum_probs=29.3
Q ss_pred cCCCCCC--CCcceeecCCCCc--eEecCCCcccccccccccc
Q 014105 298 NSKPCPR--CKRPIEKNQGCMH--MTCTPPCKFEFCWLCLGQW 336 (430)
Q Consensus 298 ~tk~CP~--C~~~IeK~~GCnh--m~C~~~C~~~FCw~C~~~~ 336 (430)
+.+.||+ |...|++..|.++ |+|. .|++.|||.|+++|
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~-~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCP-SCGTEFCFKCGEPW 58 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTT-SCCSEECSSSTSES
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECC-CCCCcCccccCccc
Confidence 3489988 9999999999999 9998 89999999999998
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.08 E-value=2.8e-06 Score=58.33 Aligned_cols=42 Identities=40% Similarity=1.036 Sum_probs=34.1
Q ss_pred cccccccccc-CCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCC
Q 014105 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (430)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (430)
.|+||++.+. ...++.++|||.||..|+.... + ..+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~------~---~~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK------G---KSVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc------C---CCCCCc--CCC
Confidence 4999999993 3467888999999999999888 2 157899 675
No 17
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.06 E-value=3.2e-06 Score=59.67 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=36.8
Q ss_pred ccccccccccccCCCeeeccCCCc-ccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
...|.||++.. ..++.++|||. ||..|+..++.. ..+|| .|+..+.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~---------~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR---------KKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT---------TSBBT--TTTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc---------CCCCC--cCChhhc
Confidence 45799999975 57888999999 999999999982 35899 8988764
No 18
>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=98.03 E-value=5.5e-06 Score=56.31 Aligned_cols=44 Identities=34% Similarity=0.986 Sum_probs=33.6
Q ss_pred ccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 143 TCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
+|+||++.+ .......+|||.||..|+..|+.. + ..+|| .|+..
T Consensus 1 ~C~iC~~~~-~~~~~~~~C~H~~c~~C~~~~~~~----~----~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF-REPVVLLPCGHVFCRSCIDKWLKS----G----KNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh-hCceEecCCCChhcHHHHHHHHHh----C----cCCCC--CCCCc
Confidence 499999987 233444559999999999999876 2 45799 78764
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=2.7e-06 Score=77.75 Aligned_cols=60 Identities=33% Similarity=0.707 Sum_probs=49.5
Q ss_pred CCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhc
Q 014105 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLS 207 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll 207 (430)
....|+|.||++.- .+++...|||.||..||-+|+.+..+. -.|| .|+..+..+.|-.|.
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~------~~cP--VCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS------KECP--VCKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC------eeCC--ccccccccceEEeee
Confidence 46789999999974 788999999999999999999986543 3588 899998877665544
No 20
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=8.5e-06 Score=76.70 Aligned_cols=53 Identities=30% Similarity=0.688 Sum_probs=43.7
Q ss_pred CCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
......|.+|++.. ..+..++|||.||..|+..|...+- .|| .|+..+.+..|
T Consensus 236 ~~a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek~---------eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 236 PEATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEKA---------ECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHcccc---------CCC--cccccCCCcce
Confidence 34567899999975 6888999999999999999998742 499 89998876554
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=6.8e-06 Score=79.85 Aligned_cols=109 Identities=25% Similarity=0.493 Sum_probs=64.4
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcChHHHHHHHHH
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRY 218 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~~ 218 (430)
...++|+||++.+ ..+..++|||.||..|+...+. + .+.|| .|+. ... .+...-........
T Consensus 11 ~~~~~C~iC~~~~--~~p~~l~C~H~~c~~C~~~~~~-----~----~~~Cp--~cr~-~~~----~~~~n~~l~~~~~~ 72 (386)
T KOG2177|consen 11 QEELTCPICLEYF--REPVLLPCGHNFCRACLTRSWE-----G----PLSCP--VCRP-PSR----NLRPNVLLANLVER 72 (386)
T ss_pred cccccChhhHHHh--hcCccccccchHhHHHHHHhcC-----C----CcCCc--ccCC-chh----ccCccHHHHHHHHH
Confidence 3578899999998 4458889999999999999998 2 58999 8884 222 22211111111111
Q ss_pred HHHHHHhcC-C-CceecCCCCCCceEEeecCCCCceEEe-cCCCccccccC-CcCCCCCCch
Q 014105 219 FIRSYVEDN-R-KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCT-EEAHRPVDCD 276 (430)
Q Consensus 219 ~~~~~v~~~-~-~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~-~~~H~~~~C~ 276 (430)
+...-.... . ....|+. ......+.| .|....|..|. ...|..+.-.
T Consensus 73 ~~~~~~~~~~~~~~~~c~~-----------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~ 123 (386)
T KOG2177|consen 73 LRQLRLSRPLGSKEELCEK-----------HGEELKLFCEEDEKLLCVLCRESGEHRGHPVL 123 (386)
T ss_pred HHhcCCcccccccchhhhh-----------cCCcceEEecccccccCCCCCCcccccCCccc
Confidence 110000000 0 0002332 111256789 89999999998 6677766443
No 22
>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=97.82 E-value=2.1e-05 Score=58.16 Aligned_cols=48 Identities=13% Similarity=0.239 Sum_probs=39.1
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhH
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~ 202 (430)
+.|+||.+.+ .+++.++|||.||+.|+..|+.. + ..|| .|+..++...
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~----~-----~~cP--~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS----H-----GTDP--VTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH----C-----CCCC--CCcCCCChhh
Confidence 5799999976 56888999999999999999976 1 2698 6887775544
No 23
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.76 E-value=2.3e-05 Score=51.20 Aligned_cols=30 Identities=37% Similarity=1.009 Sum_probs=26.7
Q ss_pred cccccccccCCCeeeccCCCcccHHHHHHHHH
Q 014105 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (430)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~ 175 (430)
|+||++.. ..++.++|||.||..|+..|+.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH
Confidence 78999873 6778889999999999999988
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.1e-05 Score=81.46 Aligned_cols=58 Identities=28% Similarity=0.662 Sum_probs=44.7
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhh
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLL 206 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~l 206 (430)
...||||++.. .-++.+.|||.||..||.+||......+ ..+|| -|...|....+..+
T Consensus 186 ~~~CPICL~~~--~~p~~t~CGHiFC~~CiLqy~~~s~~~~----~~~CP--iC~s~I~~kdl~pv 243 (513)
T KOG2164|consen 186 DMQCPICLEPP--SVPVRTNCGHIFCGPCILQYWNYSAIKG----PCSCP--ICRSTITLKDLLPV 243 (513)
T ss_pred CCcCCcccCCC--CcccccccCceeeHHHHHHHHhhhcccC----CccCC--chhhhccccceeee
Confidence 67899999864 3455566999999999999999873333 57899 89988876554433
No 25
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.73 E-value=2.6e-05 Score=73.06 Aligned_cols=50 Identities=24% Similarity=0.615 Sum_probs=37.4
Q ss_pred CCccccccccccccCCC------eeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 139 GEEMTCGICFENYPSDR------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
+...+|+||++.+.... .+.++|+|.||..|+..|+.. ...|| .|+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~---------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE---------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc---------CCCCC--CCCCEee
Confidence 34678999999864322 245579999999999998764 23799 8998764
No 26
>PHA02926 zinc finger-like protein; Provisional
Probab=97.71 E-value=2.7e-05 Score=70.74 Aligned_cols=56 Identities=34% Similarity=0.670 Sum_probs=40.4
Q ss_pred CCccccccccccccC-----C--CeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 139 GEEMTCGICFENYPS-----D--RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~-----~--~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
+...+|+||++..-. . -.+..+|+|.||..|++.|-.++...|. .-.|| .|+..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~---~rsCP--iCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGA---SDNCP--ICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCc---CCcCC--CCcceee
Confidence 456889999987521 1 1244579999999999999987543332 45799 8998653
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.69 E-value=2.7e-05 Score=78.10 Aligned_cols=65 Identities=25% Similarity=0.542 Sum_probs=46.6
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH-HhhcChHHHHHHH
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI-YLLSSDEDKVKYN 216 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i-~~ll~~e~~~ky~ 216 (430)
...+.|+||++.+ ..++.++|||.||..|+..|+.. ...|| .|+..+....+ ...+-.++++.|.
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~---------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSN---------QPKCP--LCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhC---------CCCCC--CCCCccccccCccchHHHHHHHHHH
Confidence 3468999999987 66778899999999999999864 12699 89988754322 2222234555554
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.48 E-value=9.1e-05 Score=70.97 Aligned_cols=62 Identities=31% Similarity=0.670 Sum_probs=47.9
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHh-hcChHHHHHH
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYL-LSSDEDKVKY 215 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~-ll~~e~~~ky 215 (430)
.+-|.||++.| .-++.++|+|.||.-|++.|+.. ...|| .|...+.+..++. .+-.++++-|
T Consensus 23 lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~---------~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 23 LLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSY---------KPQCP--TCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHhHHHHHh--cCceeccccchHHHHHHHHHhcc---------CCCCC--ceecccchhhhhhhhHHHHHHHHH
Confidence 46799999988 56777889999999999999986 34799 8999887776653 3334555554
No 29
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.32 E-value=0.00013 Score=71.95 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=29.4
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHH
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~ 175 (430)
+++.|+||..-| .+++.++|+|..|+.|-+.-+.
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhcc
Confidence 467899999877 7899999999999999987654
No 30
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=8.8e-05 Score=78.62 Aligned_cols=55 Identities=29% Similarity=0.739 Sum_probs=45.3
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhh
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLL 206 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~l 206 (430)
..++||+|.... .+.+...|||.||..|++..+.+.- =+|| .|+..|+...|..+
T Consensus 642 ~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etRq--------RKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETRQ--------RKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHhc--------CCCC--CCCCCCCccccccc
Confidence 467999998543 6778889999999999999998853 3899 99999988777543
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.04 E-value=0.0011 Score=64.14 Aligned_cols=51 Identities=24% Similarity=0.603 Sum_probs=36.8
Q ss_pred cccccccccccC-CC---eeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 142 MTCGICFENYPS-DR---LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 142 ~~C~IC~e~~~~-~~---~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
..||||...... .. ++. +|||.||..|+...|.. | +..|| .|+..+....+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~----~----~~~CP--~C~~~lrk~~f 58 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVR----G----SGSCP--ECDTPLRKNNF 58 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcC----C----CCCCC--CCCCccchhhc
Confidence 579999986322 22 223 79999999999999843 3 34899 89988766543
No 32
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.84 E-value=0.00091 Score=48.44 Aligned_cols=47 Identities=26% Similarity=0.614 Sum_probs=30.0
Q ss_pred CccccccccccccCCCee-eccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCC
Q 014105 140 EEMTCGICFENYPSDRLL-AAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~-~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (430)
..+.|||....+ .+++ +..|||.|.++.+..|+. .+ ..++||..+|.
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~----~~---~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQ----RN---GSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCT----TT---S-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHH----hc---CCCCCCCCCCC
Confidence 357899999877 5565 468999999999999992 22 26899998885
No 33
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.83 E-value=0.00097 Score=62.31 Aligned_cols=54 Identities=28% Similarity=0.528 Sum_probs=41.8
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
...+.|.||++.- ..+..++|||.||..|+...|..+- .-.|| .|++.+.+..|
T Consensus 213 ~~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~k-------~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKKK-------YEFCP--LCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeeccc--CCcccccccchhhHHHHHHHHHhhc-------cccCc--hhhhhccchhh
Confidence 4478899999864 7788899999999999998654421 33599 89988766555
No 34
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.78 E-value=0.0023 Score=48.88 Aligned_cols=50 Identities=16% Similarity=0.208 Sum_probs=37.5
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhh
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~ 201 (430)
..+.|+|+.+.+ .+++.+++||.|++.++..|+.. + ...|| .++..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~----~----~~~~P--~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ----N----GGTDP--FTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT----T----SSB-T--TT-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc----C----CCCCC--CCCCcCCcc
Confidence 468999999877 78999999999999999999987 1 34788 677777654
No 35
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.00091 Score=63.43 Aligned_cols=51 Identities=29% Similarity=0.735 Sum_probs=42.3
Q ss_pred CccccccccccccC-CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
...+|.||++.+.. +....+||.|.|...|+.+|+.. ...+|| .|+..+++
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~--------y~~~CP--vCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG--------YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh--------hcccCC--ccCCCCCC
Confidence 45789999999864 45678899999999999999974 256899 89998875
No 36
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.72 E-value=0.00084 Score=67.96 Aligned_cols=57 Identities=25% Similarity=0.781 Sum_probs=46.3
Q ss_pred CCCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhh
Q 014105 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (430)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~ 201 (430)
.+.....|.+|-+.- .+.+...|.|.||+-|++.|+....... .+.|| .|...++.+
T Consensus 532 enk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~----nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN----NVTCP--VCHIGLSID 588 (791)
T ss_pred cccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc----CCCCc--ccccccccc
Confidence 356688999998854 6777889999999999999999876543 58999 898877554
No 37
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.63 E-value=0.004 Score=42.35 Aligned_cols=41 Identities=22% Similarity=0.427 Sum_probs=34.8
Q ss_pred HHHHHHHHhHcCCCHHHHHHHHHhcCCChhhhhhhhhhcHH
Q 014105 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEE 120 (430)
Q Consensus 80 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~ 120 (430)
++.|.+..++.++++..|..+|...+||++..++.||.+++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 36788999999999999999999999999999999998643
No 38
>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=96.61 E-value=0.0021 Score=49.15 Aligned_cols=35 Identities=26% Similarity=0.606 Sum_probs=26.5
Q ss_pred cccccccccccC-----------CCeeeccCCCcccHHHHHHHHHh
Q 014105 142 MTCGICFENYPS-----------DRLLAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 142 ~~C~IC~e~~~~-----------~~~~~l~CgH~fC~~Cl~~yi~~ 176 (430)
-.|.||++.+.. -.+...+|||.|...|+.+|+..
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc
Confidence 359999998821 12334579999999999999966
No 39
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.53 E-value=0.00042 Score=50.68 Aligned_cols=45 Identities=33% Similarity=0.788 Sum_probs=21.5
Q ss_pred ccccccccccccCCCeeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 141 EMTCGICFENYPSDRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
.+.|++|.+.+ ..++.+ .|.|.||..|++..+. -.|| .|..+.-.
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~-----------~~CP--vC~~Paw~ 52 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG-----------SECP--VCHTPAWI 52 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT-----------TB-S--SS--B-S-
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC-----------CCCC--CcCChHHH
Confidence 35699999876 667654 6999999999966332 2499 88876533
No 40
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.45 E-value=0.0027 Score=62.47 Aligned_cols=47 Identities=30% Similarity=0.782 Sum_probs=39.0
Q ss_pred cccccccccccCC-CeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 142 MTCGICFENYPSD-RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 142 ~~C~IC~e~~~~~-~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.+|.||+|.|... .+..|||+|.|...|+..|+... + -.|| .|+..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r-----~~CP--vCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---R-----TFCP--VCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---C-----ccCC--CCCCcC
Confidence 6999999999754 57789999999999999999874 2 2599 788754
No 41
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.0039 Score=61.73 Aligned_cols=40 Identities=35% Similarity=0.980 Sum_probs=36.1
Q ss_pred hcCCCCCC--CCcceeecCCCCceEecCCCccccccccccccc
Q 014105 297 ANSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (430)
Q Consensus 297 ~~tk~CP~--C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (430)
++..-||+ |..|+-...|++-..|. +|.+.||.+|...|.
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~Cs-kCnFaFCtlCk~t~H 312 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICS-KCNFAFCTLCKLTWH 312 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhc-cCccHHHHHHHHhhc
Confidence 46799998 99999777899999999 899999999998874
No 42
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.34 E-value=0.0023 Score=60.30 Aligned_cols=63 Identities=25% Similarity=0.432 Sum_probs=43.4
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHh-hcChHHHHHHH
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYL-LSSDEDKVKYN 216 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~-ll~~e~~~ky~ 216 (430)
..-|-||-+.+ .-+...+|||.||.-|++.|+.++ .-|| .|....-...++. .+..++.+-|.
T Consensus 25 ~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~q---------p~CP--~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 25 MLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGTQ---------PFCP--VCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred HHHhhhhhhee--ecceecccccchhHHHHHHHhcCC---------CCCc--cccccHHhhhcccchhHHHHHHhhh
Confidence 56799998876 556778999999999999999762 3588 7877654433322 23334444444
No 43
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.20 E-value=0.016 Score=56.55 Aligned_cols=93 Identities=18% Similarity=0.314 Sum_probs=55.1
Q ss_pred HHHHHHHhcCCChhhhhhhhhhcHHHHHHHhCCC---CCCCcCCCCCCccccccccccc-cCC----------CeeeccC
Q 014105 96 AASILLRFYNWSVSKVHDEWFADEERVRKAVGLL---EKPAVQFPDGEEMTCGICFENY-PSD----------RLLAAAC 161 (430)
Q Consensus 96 ~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~gl~---~~~~~~~~~~~~~~C~IC~e~~-~~~----------~~~~l~C 161 (430)
....|+|.--|....|..+..+-..-.|....+. +...++.-.....+|.||+++. ... .+..++|
T Consensus 239 ~Pi~l~r~~~t~~~AL~~~i~~~~~~~r~~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpC 318 (491)
T COG5243 239 VPIYLIRQMYTCFYALFRRIREHARFRRATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPC 318 (491)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccc
Confidence 4466777777777666544322111111111111 1101111134467899999983 221 3578999
Q ss_pred CCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 162 GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 162 gH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
||.+...|++.|++.+ -.|| -|+.++-
T Consensus 319 GHilHl~CLknW~ERq---------QTCP--ICr~p~i 345 (491)
T COG5243 319 GHILHLHCLKNWLERQ---------QTCP--ICRRPVI 345 (491)
T ss_pred cceeeHHHHHHHHHhc---------cCCC--cccCccc
Confidence 9999999999999873 3699 7988753
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.83 E-value=0.0045 Score=46.90 Aligned_cols=58 Identities=21% Similarity=0.632 Sum_probs=26.9
Q ss_pred cccccccccccc-CCCe--ee---ccCCCcccHHHHHHHHHhhhcCCCce--eecccCCCCCCCCchh
Q 014105 141 EMTCGICFENYP-SDRL--LA---AACGHPFCSSCWTGYISTAINDGPGC--LMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 141 ~~~C~IC~e~~~-~~~~--~~---l~CgH~fC~~Cl~~yi~~~i~~g~~~--~~i~CP~~~C~~~l~~ 200 (430)
...|+||+..+. .... +. ..|++.|...||.+|+...-...... ..=.|| .|+..|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 467999998754 2222 12 25899999999999998765543211 123699 89987753
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.71 E-value=0.0074 Score=41.76 Aligned_cols=45 Identities=24% Similarity=0.718 Sum_probs=21.6
Q ss_pred cccccccccCC--CeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 144 CGICFENYPSD--RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 144 C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
|++|.+.+... .+...+||+.+|+.||..-... + .=+|| +|+...
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~----~----~g~CP--gCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN----E----GGRCP--GCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS----S-----SB-T--TT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc----c----CCCCC--CCCCCC
Confidence 78999887544 3445569999999999876652 2 12799 898653
No 46
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.37 E-value=0.017 Score=54.29 Aligned_cols=52 Identities=27% Similarity=0.623 Sum_probs=39.3
Q ss_pred CCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
.+...+|++|.+. |....+..+|||.||--|+..-..... .+.|| .|+..+.
T Consensus 236 ~t~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~a-------sf~Cp--~Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWDA-------SFTCP--LCGENVE 287 (298)
T ss_pred ccCCceeeccCCC-CCCCeeeccccceeehhhhhhhhcchh-------hcccC--ccCCCCc
Confidence 3457899999864 444555667999999999998776532 57999 8998765
No 47
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.36 E-value=0.0083 Score=57.16 Aligned_cols=54 Identities=20% Similarity=0.522 Sum_probs=41.6
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHH
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY 204 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~ 204 (430)
.....|.||+.+- .-++.+.|+|.||.-|+++-+.. + ...|| .|+..|+...+.
T Consensus 5 ~~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----d----k~~Ca--vCR~pids~i~~ 58 (324)
T KOG0824|consen 5 TKKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----D----KKTCA--VCRFPIDSTIDF 58 (324)
T ss_pred ccCCcceeeeccC--CcCccccccchhhhhhhcchhhc----C----CCCCc--eecCCCCcchhc
Confidence 3456799999875 56789999999999999976544 2 34598 899988766543
No 48
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.17 E-value=0.0072 Score=53.96 Aligned_cols=34 Identities=35% Similarity=0.863 Sum_probs=28.5
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHH
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~ 175 (430)
-.|.|.||-.+| ..++...|||.||..|...-..
T Consensus 195 IPF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 195 IPFLCGICKKDY--ESPVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred Cceeehhchhhc--cchhhhhcchhHHHHHHHHHhc
Confidence 368999999988 6788899999999999865443
No 49
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.16 E-value=0.024 Score=57.22 Aligned_cols=49 Identities=24% Similarity=0.714 Sum_probs=38.1
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
...+.|.||+..+ ..++.++|||.||..|+.+ .+.. ...|| .|+..+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r----~ld~-----~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDR----SLDQ-----ETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHH----Hhcc-----CCCCc--cccccccc
Confidence 5689999999877 6778889999999999777 2222 34788 69987753
No 50
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.02 E-value=0.14 Score=51.44 Aligned_cols=116 Identities=23% Similarity=0.359 Sum_probs=65.8
Q ss_pred ecHHHHHHHHHHHHHHHHhHcCCCHH--HHHHHHHhcCCChhh--hhhhhh----h--cHHHHHH-----HhCCCC--CC
Q 014105 70 LTEADIRQRQEEDITRISTVLSISKV--AASILLRFYNWSVSK--VHDEWF----A--DEERVRK-----AVGLLE--KP 132 (430)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~~l~i~~~--~a~~LL~~~~W~~~~--l~~~~~----~--~~~~~~~-----~~gl~~--~~ 132 (430)
||..||.+.+..-+..|+.+.=|-.+ .-.++|..|+=..+. ..+.|- + +++ +.. .+.+.. ..
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Chll~V~~ve~~~s~d~ 164 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCHLLYVDRVEVTESEDG 164 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-ceeEEEEEEEEEEecccC
Confidence 78999999999888888877655421 223444455433221 111110 0 011 110 011111 11
Q ss_pred Cc--CCCCCCccccccccccccC--CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 133 AV--QFPDGEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 133 ~~--~~~~~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
.. +....+..|||||++.... +-+++..|.|.|--.|+..|+.. +|| .|+....
T Consensus 165 as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~-----------scp--vcR~~q~ 222 (493)
T KOG0804|consen 165 ASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS-----------SCP--VCRYCQS 222 (493)
T ss_pred CCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccC-----------cCh--hhhhhcC
Confidence 11 1112456799999998753 34567789999999999888643 688 7775443
No 51
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.53 E-value=0.027 Score=55.76 Aligned_cols=59 Identities=24% Similarity=0.584 Sum_probs=39.8
Q ss_pred CCCCCccccccccccccCCC-----eee-ccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 136 FPDGEEMTCGICFENYPSDR-----LLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 136 ~~~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.+.....+|+||++...... +-. .+|.|.||..|++.|=...-... ...-.|| .|+...
T Consensus 156 ~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~--~~sksCP--~CRv~s 220 (344)
T KOG1039|consen 156 LQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFES--KTSKSCP--FCRVPS 220 (344)
T ss_pred cCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcccc--ccccCCC--cccCcc
Confidence 34567889999999864332 223 45999999999999874432221 1356799 788653
No 52
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=94.52 E-value=0.015 Score=56.13 Aligned_cols=48 Identities=29% Similarity=0.710 Sum_probs=36.2
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
..++|.+|-.-+. +......|-|.||+.||..|+.. ...|| .|...+.
T Consensus 14 ~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~---------~~~CP--~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEE---------SKYCP--TCDIVIH 61 (331)
T ss_pred cceehhhccceee-cchhHHHHHHHHHHHHHHHHHHH---------hccCC--ccceecc
Confidence 4678999986552 33344569999999999999998 13699 7887653
No 53
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.077 Score=50.90 Aligned_cols=95 Identities=23% Similarity=0.601 Sum_probs=55.1
Q ss_pred cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcChHHHHHHHHHHHHHHHhcCCCceecCCCCCC
Q 014105 160 ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCD 239 (430)
Q Consensus 160 ~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~ 239 (430)
.||-.||+.|+..|-.-.-..+-+.. -...|...+.+... ...+|..... ..| ....+.||. |.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as----~t~tc~y~vde~~a-------~~arwd~as~-~TI--k~tTkpCPk--Ch 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEAS----GTTTCAYRVDERAA-------EQARWDAASK-ETI--KKTTKPCPK--CH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccc----cccceeeecChhhh-------hhhhhhhhhh-hhh--hhccCCCCC--cc
Confidence 39999999999988654322211000 01134444433221 1233433221 122 234577885 88
Q ss_pred ceEEeecCCCCceEEe-c--CCCccccccCCcCCCC
Q 014105 240 YAVDFVVGSGNYDVTC-R--CSYSFCWNCTEEAHRP 272 (430)
Q Consensus 240 ~~i~~~~~~~~~~v~C-~--C~~~fC~~C~~~~H~~ 272 (430)
.+.+.. .+-..+.| . ||..+||+|+.+|.+.
T Consensus 405 vptErn--GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 405 VPTERN--GGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred CccccC--CceEEeecCCCCCCceeEeccCChhhhh
Confidence 776553 45677889 4 9999999999888653
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.78 E-value=0.043 Score=51.53 Aligned_cols=72 Identities=18% Similarity=0.463 Sum_probs=50.8
Q ss_pred HHHHHhCCCCCCCcCCCCCCccccccccccccC--------CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCC
Q 014105 121 RVRKAVGLLEKPAVQFPDGEEMTCGICFENYPS--------DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDP 192 (430)
Q Consensus 121 ~~~~~~gl~~~~~~~~~~~~~~~C~IC~e~~~~--------~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~ 192 (430)
.+...+|.-.++..+....+...|.||-..+.. +++..++|+|.|...|+++|... |+ .-.||
T Consensus 204 ~mAs~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK---kqtCP-- 274 (328)
T KOG1734|consen 204 YMASTIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK---KQTCP-- 274 (328)
T ss_pred HHHHHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC---CCCCc--
Confidence 344455665444444444566789999876543 25678999999999999999876 33 45799
Q ss_pred CCCCCchhh
Q 014105 193 SCGAAVGQD 201 (430)
Q Consensus 193 ~C~~~l~~~ 201 (430)
-|+..+...
T Consensus 275 YCKekVdl~ 283 (328)
T KOG1734|consen 275 YCKEKVDLK 283 (328)
T ss_pred hHHHHhhHh
Confidence 899877543
No 55
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.75 E-value=0.01 Score=57.80 Aligned_cols=48 Identities=25% Similarity=0.662 Sum_probs=34.7
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..+.|+||++.+. .-+....|+|.||.+|+-.-+.. | .-.|| .|+..+
T Consensus 42 ~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~----g----n~ecp--tcRk~l 89 (381)
T KOG0311|consen 42 IQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS----G----NNECP--TCRKKL 89 (381)
T ss_pred hhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh----c----CCCCc--hHHhhc
Confidence 4678999998763 23444569999999998766654 2 23799 888754
No 56
>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=93.65 E-value=0.034 Score=33.38 Aligned_cols=24 Identities=29% Similarity=0.945 Sum_probs=15.8
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
|.||.|+..|-.+ -..|. .||+.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp-~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCP-HCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCC-CCCCCC
Confidence 5789998888422 25565 677766
No 57
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.64 E-value=0.098 Score=52.00 Aligned_cols=49 Identities=31% Similarity=0.844 Sum_probs=38.6
Q ss_pred ccccccccccccC---CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 141 EMTCGICFENYPS---DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 141 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..+||||++.+.. ..++++.|||.|=.+|+++|+. ++ ...+|| .|...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~------~~~~cp--~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK------TKMQCP--LCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh------hhhhCc--ccCChh
Confidence 3589999998642 3578899999999999999994 33 357899 787654
No 58
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.63 E-value=0.076 Score=41.45 Aligned_cols=34 Identities=26% Similarity=0.594 Sum_probs=26.3
Q ss_pred eeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 157 LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 157 ~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
+.-.|+|.|...|+.+++.++-.. -.|| -|+..+
T Consensus 48 v~g~C~H~FH~hCI~kWl~~~~~~------~~CP--mCR~~w 81 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILKWLSTQSSK------GQCP--MCRQPW 81 (85)
T ss_pred eeccCccHHHHHHHHHHHccccCC------CCCC--CcCCee
Confidence 334699999999999999986322 2799 788765
No 59
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.047 Score=58.06 Aligned_cols=46 Identities=30% Similarity=0.720 Sum_probs=36.5
Q ss_pred ccccccccccccCC---CeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 141 EMTCGICFENYPSD---RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 141 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
...|.||.+.+... .+..++|+|.|+..|++.|++.+ -.|| .|+..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~---------qtCP--~CR~~ 339 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ---------QTCP--TCRTV 339 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHh---------CcCC--cchhh
Confidence 66899999987431 26788999999999999999982 2688 67763
No 60
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=92.27 E-value=0.45 Score=46.16 Aligned_cols=49 Identities=24% Similarity=0.630 Sum_probs=35.9
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..-.|+||+... .++.+...-|-.||-.|+..|+.. .| +||..+|+..+
T Consensus 299 ~~~~CpvClk~r-~Nptvl~vSGyVfCY~Ci~~Yv~~---~~------~CPVT~~p~~v 347 (357)
T KOG0826|consen 299 DREVCPVCLKKR-QNPTVLEVSGYVFCYPCIFSYVVN---YG------HCPVTGYPASV 347 (357)
T ss_pred ccccChhHHhcc-CCCceEEecceEEeHHHHHHHHHh---cC------CCCccCCcchH
Confidence 356799999765 234444457999999999999984 33 69987777544
No 61
>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=91.92 E-value=0.18 Score=47.17 Aligned_cols=6 Identities=17% Similarity=0.528 Sum_probs=2.5
Q ss_pred cCcCCC
Q 014105 20 DFYSGG 25 (430)
Q Consensus 20 ~~~~~~ 25 (430)
++|++.
T Consensus 259 ~~~~~~ 264 (314)
T PF06524_consen 259 GYYGDY 264 (314)
T ss_pred cccCcc
Confidence 344443
No 62
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.92 E-value=0.16 Score=49.89 Aligned_cols=64 Identities=19% Similarity=0.479 Sum_probs=43.6
Q ss_pred HHhCCCCCCCcCCC---CCCccccccccccccCCCeeeccCCCc-ccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 124 KAVGLLEKPAVQFP---DGEEMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 124 ~~~gl~~~~~~~~~---~~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
...||.++...... +.....|-||+.+. .+.+.|||.|. .|.+|-+..- ...+ +|| -|+..|.
T Consensus 270 EiyGien~~v~~~~~~~~~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr---~q~n------~CP--ICRqpi~ 336 (349)
T KOG4265|consen 270 EIYGIENSTVEGTDADESESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR---YQTN------NCP--ICRQPIE 336 (349)
T ss_pred hhhccccCCCCCCccccccCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH---Hhhc------CCC--ccccchH
Confidence 34466544332222 14467899999875 78899999997 8999988665 2222 699 8998764
Q ss_pred h
Q 014105 200 Q 200 (430)
Q Consensus 200 ~ 200 (430)
.
T Consensus 337 ~ 337 (349)
T KOG4265|consen 337 E 337 (349)
T ss_pred h
Confidence 3
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=91.02 E-value=0.42 Score=54.43 Aligned_cols=73 Identities=22% Similarity=0.446 Sum_probs=53.8
Q ss_pred ccccccccccc-cCCCeeeccCCCcccHHHHHHHHHhhhcCCCce--eecccCCCCCCCCchhhHHHhhcChHHHHHHHH
Q 014105 141 EMTCGICFENY-PSDRLLAAACGHPFCSSCWTGYISTAINDGPGC--LMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (430)
Q Consensus 141 ~~~C~IC~e~~-~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~--~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~ 217 (430)
.-.|.|||.+- .....+.+.|+|.|...|.+..++.+-. |+++ ..|.|| -|...|..-.++.|+.+ +++.|+.
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~-GPRItF~FisCP--iC~n~InH~~LkDLldP-iKel~ed 3561 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWL-GPRITFGFISCP--ICKNKINHIVLKDLLDP-IKELYED 3561 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhccc-CCeeEEeeeecc--cccchhhhHHHHHHHHH-HHHHHHH
Confidence 45799999763 3445678899999999999999988765 4322 368999 89999988888777763 3344443
No 64
>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=90.99 E-value=0.26 Score=34.39 Aligned_cols=36 Identities=19% Similarity=0.462 Sum_probs=28.0
Q ss_pred ccccccccccCCCeeeccCC-----CcccHHHHHHHHHhhh
Q 014105 143 TCGICFENYPSDRLLAAACG-----HPFCSSCWTGYISTAI 178 (430)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~Cl~~yi~~~i 178 (430)
.|-||++.....++...||. |.+...|+..|+..+-
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC
Confidence 38899984444566777875 8899999999998753
No 65
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.80 E-value=0.19 Score=35.35 Aligned_cols=27 Identities=26% Similarity=0.719 Sum_probs=20.8
Q ss_pred CCCCCCCcceeecC--CCCceEecCCCccc
Q 014105 300 KPCPRCKRPIEKNQ--GCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~IeK~~--GCnhm~C~~~C~~~ 327 (430)
+.||.|+.++.... +-++..|+ .||+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~-~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCR-KCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECC-cCCCe
Confidence 46999999887553 35689998 79875
No 66
>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=90.38 E-value=0.13 Score=43.60 Aligned_cols=34 Identities=26% Similarity=0.701 Sum_probs=28.3
Q ss_pred ccccccccccccC-CCeeeccCC------CcccHHHHHHHH
Q 014105 141 EMTCGICFENYPS-DRLLAAACG------HPFCSSCWTGYI 174 (430)
Q Consensus 141 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~Cl~~yi 174 (430)
..+|.||++.+.. .-++.++|| |.||.+|+++|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 6789999999876 456777786 679999999994
No 67
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.27 E-value=0.21 Score=48.74 Aligned_cols=53 Identities=30% Similarity=0.640 Sum_probs=38.7
Q ss_pred CCCCCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 135 QFPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 135 ~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
..|.++.-.|+||+-. +-.-+..||+|.-|..|+.+|+-.. -+|- -|+..+..
T Consensus 416 ~lp~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN~---------k~CF--fCktTv~~ 468 (489)
T KOG4692|consen 416 DLPDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMNC---------KRCF--FCKTTVID 468 (489)
T ss_pred CCCCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhcC---------Ceee--Eecceeee
Confidence 3566778899999863 2344667999999999999998652 2455 68876643
No 68
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.06 E-value=1.5 Score=43.83 Aligned_cols=56 Identities=16% Similarity=0.351 Sum_probs=40.2
Q ss_pred CccccccccccccC-CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
+-|.|||=-+.-.. +.|..+.|||.++++=+.+.... |. ..++|| -|+........
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~n----g~--~sfKCP--YCP~e~~~~~~ 389 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKN----GS--QSFKCP--YCPVEQLASDT 389 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhC----CC--eeeeCC--CCCcccCHHhc
Confidence 47899996655433 56788999999999987766543 32 379999 89876554433
No 69
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.02 E-value=0.11 Score=48.46 Aligned_cols=46 Identities=28% Similarity=0.691 Sum_probs=33.7
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
+.|..|+---+...++.+.|+|.||..|.+.-. +-.|| .|+..+..
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~-----------~~~C~--lCkk~ir~ 49 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS-----------PDVCP--LCKKSIRI 49 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC-----------ccccc--cccceeee
Confidence 569999876555667788999999999974311 22798 89987643
No 70
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.92 E-value=0.4 Score=48.68 Aligned_cols=42 Identities=26% Similarity=0.827 Sum_probs=34.1
Q ss_pred CCceecCCCCCCceEEeecCCCCceEEecCCCccccccCCcCCCCC
Q 014105 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPV 273 (430)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~ 273 (430)
...+.||. |...+... .+-..++|.|++.||+.|+.+|+...
T Consensus 304 ~~wr~Cpk--C~~~ie~~--~GCnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCPK--CKFMIELS--EGCNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCcc--cceeeeec--CCcceEEeeccccchhhcCcchhhCC
Confidence 55788995 99888664 45788999999999999998886554
No 71
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.84 E-value=0.17 Score=29.42 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=7.9
Q ss_pred CCCCCCccee
Q 014105 301 PCPRCKRPIE 310 (430)
Q Consensus 301 ~CP~C~~~Ie 310 (430)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 4888888886
No 72
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.67 E-value=0.51 Score=46.04 Aligned_cols=56 Identities=27% Similarity=0.617 Sum_probs=41.3
Q ss_pred ccccccccccccCC----CeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC--chhhHHHhh
Q 014105 141 EMTCGICFENYPSD----RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA--VGQDMIYLL 206 (430)
Q Consensus 141 ~~~C~IC~e~~~~~----~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~--l~~~~i~~l 206 (430)
...|.||-++|... -|..+.|||.+|..|+...+.. ..+.|| .|+.+ ++...+..+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~--------~~i~cp--fcR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN--------SRILCP--FCRETTEIPDGDVKSL 64 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC--------ceeecc--CCCCcccCCchhHhhh
Confidence 45799999998754 3456779999999999988865 256787 89987 444445444
No 73
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.44 E-value=0.2 Score=51.02 Aligned_cols=51 Identities=24% Similarity=0.561 Sum_probs=37.5
Q ss_pred CccccccccccccCC-----C----------eeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 140 EEMTCGICFENYPSD-----R----------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~-----~----------~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
....|.||+.+++.. . ....||.|.|.+.|+.+|..+ ..+.|| .|+.++++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~--------ykl~CP--vCR~pLPp 635 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT--------YKLICP--VCRCPLPP 635 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh--------hcccCC--ccCCCCCC
Confidence 466899999876431 1 113489999999999999985 246799 78877653
No 74
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.80 E-value=0.23 Score=29.70 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=8.7
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
+.||+|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 67888888775
No 75
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.76 E-value=0.15 Score=48.73 Aligned_cols=45 Identities=29% Similarity=0.685 Sum_probs=35.6
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.+-|.||-..| ..++...|+|.||..|....+.. + -+|+ .|...+
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk----~-----~~c~--vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK----G-----EKCY--VCSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc----C-----Ccce--eccccc
Confidence 56799999887 77888999999999998776654 2 3676 677654
No 76
>PHA00626 hypothetical protein
Probab=88.44 E-value=0.36 Score=34.24 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=21.0
Q ss_pred CCCCCCc-ceeecCCCCc----eEecCCCccccc
Q 014105 301 PCPRCKR-PIEKNQGCMH----MTCTPPCKFEFC 329 (430)
Q Consensus 301 ~CP~C~~-~IeK~~GCnh----m~C~~~C~~~FC 329 (430)
.||+|+. -|.|.+-|+. ..|. .||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCk-dCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCC-DCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcC-CCCCeec
Confidence 5999998 4878777654 6777 7887774
No 77
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=88.38 E-value=0.32 Score=52.55 Aligned_cols=11 Identities=18% Similarity=0.283 Sum_probs=8.1
Q ss_pred ccccccccccc
Q 014105 325 KFEFCWLCLGQ 335 (430)
Q Consensus 325 ~~~FCw~C~~~ 335 (430)
+..||-.||.+
T Consensus 40 ~~~fC~~CG~~ 50 (645)
T PRK14559 40 DEAHCPNCGAE 50 (645)
T ss_pred ccccccccCCc
Confidence 45589999865
No 78
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=88.26 E-value=0.2 Score=33.72 Aligned_cols=32 Identities=25% Similarity=0.626 Sum_probs=22.0
Q ss_pred CCCCCcceeecCCCCceEecCCCccccccccccccccCC
Q 014105 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
||-|...+. +.++=. |||.||..|+..|....
T Consensus 1 CpiC~~~~~-----~Pv~l~--CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLP--CGHSFCRSCLERLWKEP 32 (42)
T ss_dssp ETTTTSB-S-----SEEE-S--SSSEEEHHHHHHHHCCS
T ss_pred CCccchhhC-----CccccC--CcCHHHHHHHHHHHHcc
Confidence 566666665 556654 99999999998875443
No 79
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=87.86 E-value=0.11 Score=49.61 Aligned_cols=36 Identities=28% Similarity=0.874 Sum_probs=26.7
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCccccccccccccccCC
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
++.+|-=|-...+ |-+|+ +|||-|||-|...|-.-.
T Consensus 238 a~~kC~LCLe~~~------~pSaT-pCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 238 ATRKCSLCLENRS------NPSAT-PCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCCceEEEecCCC------CCCcC-cCcchHHHHHHHHHHccc
Confidence 4566666655553 57888 799999999999996544
No 80
>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=87.25 E-value=0.31 Score=45.08 Aligned_cols=49 Identities=27% Similarity=0.615 Sum_probs=36.3
Q ss_pred cccccccccccC-CCeeec--c-CCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 142 MTCGICFENYPS-DRLLAA--A-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 142 ~~C~IC~e~~~~-~~~~~l--~-CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..||||-.+.-. -++..+ | |-|..|.+|+-+-++. | +-.||-++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G----pAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G----PAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C----CCCCCCccHHHHH
Confidence 359999876322 233322 4 9999999999988876 4 5689999999765
No 81
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=87.16 E-value=0.79 Score=28.81 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=18.8
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCccc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
+.+-||.|+.+.....|=--|.|. .|+..
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~-~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCP-SCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEES-SSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECC-CCcCE
Confidence 458899999999988887789997 78865
No 82
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=87.15 E-value=0.23 Score=49.19 Aligned_cols=34 Identities=32% Similarity=0.740 Sum_probs=28.1
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHh
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~ 176 (430)
...|.||-+.- .++..-+|||..|..|+..|-.+
T Consensus 369 FeLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s 402 (563)
T KOG1785|consen 369 FELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS 402 (563)
T ss_pred HHHHHHhhccC--CCcccccccchHHHHHHHhhccc
Confidence 44699999863 67778899999999999988655
No 83
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=87.06 E-value=0.56 Score=47.73 Aligned_cols=37 Identities=30% Similarity=0.743 Sum_probs=30.3
Q ss_pred CCCccccccccccccCCCeee-ccCCCcccHHHHHHHHHh
Q 014105 138 DGEEMTCGICFENYPSDRLLA-AACGHPFCSSCWTGYIST 176 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~yi~~ 176 (430)
......|++|...+ .+++. +.|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc
Confidence 45578999999876 45555 589999999999998876
No 84
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=86.99 E-value=0.52 Score=29.29 Aligned_cols=27 Identities=26% Similarity=0.766 Sum_probs=15.1
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-+||+|+....-.+|.+ |.|. .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp-~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCP-ECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEET-TTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCC-cccccC
Confidence 47999999888888877 8898 799875
No 85
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=86.85 E-value=0.2 Score=48.35 Aligned_cols=37 Identities=24% Similarity=0.600 Sum_probs=25.0
Q ss_pred CceecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCC
Q 014105 229 KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRP 272 (430)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~ 272 (430)
...+|-. |+.- ........| .|...||..|..-.|..
T Consensus 329 ~~~~Cf~--C~~~-----~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 329 GSRFCFA--CQGE-----LLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCcceee--eccc-----cCCCCcEEchhccceeeccchHHHHhh
Confidence 4456764 6321 234567899 99999999998666643
No 86
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=86.52 E-value=0.27 Score=53.32 Aligned_cols=50 Identities=30% Similarity=0.755 Sum_probs=39.7
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
+.|.||.+ ...++...|+|.||.+||..+|...-. ..|| .|+..+....+
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~-------~~~~--~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN-------APCP--LCRNVLKEKKL 504 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC-------CCCc--HHHHHHHHHHH
Confidence 79999998 478888999999999999999976322 2677 88887655443
No 87
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.41 E-value=0.35 Score=33.94 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=20.8
Q ss_pred cCCCCCCCCc-ceeecCCCCceEecCCCcccc
Q 014105 298 NSKPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 298 ~tk~CP~C~~-~IeK~~GCnhm~C~~~C~~~F 328 (430)
..+.||+|+. .+.... +.++|. .||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~-~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCG-KCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECC-CcCCEE
Confidence 3479999998 444333 789999 899865
No 88
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.10 E-value=0.29 Score=34.56 Aligned_cols=45 Identities=29% Similarity=0.611 Sum_probs=33.0
Q ss_pred cccccccccccCCCeeeccCCCc-ccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 142 MTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
-+|.||++.- -+.+.-.|||. .|.+|-.+.+.. + .=.|| -|++++
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~----~----~g~CP--iCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA----L----HGCCP--ICRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc----c----CCcCc--chhhHH
Confidence 5799999852 34455679997 899999888875 1 12588 788765
No 89
>PHA03096 p28-like protein; Provisional
Probab=84.68 E-value=0.47 Score=45.94 Aligned_cols=38 Identities=24% Similarity=0.464 Sum_probs=28.9
Q ss_pred cccccccccccCC-----Ceeec-cCCCcccHHHHHHHHHhhhc
Q 014105 142 MTCGICFENYPSD-----RLLAA-ACGHPFCSSCWTGYISTAIN 179 (430)
Q Consensus 142 ~~C~IC~e~~~~~-----~~~~l-~CgH~fC~~Cl~~yi~~~i~ 179 (430)
..|+||++..... .+-.+ .|.|.||..|++.|..++..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 6899999975422 12234 49999999999999998764
No 90
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.63 E-value=0.42 Score=44.23 Aligned_cols=20 Identities=45% Similarity=1.105 Sum_probs=16.0
Q ss_pred eEecCCCccccccccccccccCC
Q 014105 318 MTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 318 m~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
+|| |||.|||=|+-.|..+.
T Consensus 62 vTl---CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL---CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee---cccceehHHHHHHHhhc
Confidence 555 99999999999997544
No 91
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=84.40 E-value=0.58 Score=34.45 Aligned_cols=25 Identities=28% Similarity=0.804 Sum_probs=10.2
Q ss_pred CCCCCCCcceeec---CCCCceEecCCCc
Q 014105 300 KPCPRCKRPIEKN---QGCMHMTCTPPCK 325 (430)
Q Consensus 300 k~CP~C~~~IeK~---~GCnhm~C~~~C~ 325 (430)
-+|++|...+... +||-|+.|+ .|-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs-~Ci 35 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCS-SCI 35 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-T-TTG
T ss_pred cCCcHHHHHhcCCceeccCccHHHH-HHh
Confidence 6899998776532 566665555 443
No 92
>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=84.33 E-value=0.5 Score=35.45 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=29.9
Q ss_pred CCCCCCcceeecCCCCceEecCCCccc-----cccccccccccCCCCCCCcccCCchh
Q 014105 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQWSDHGERTGGFYACNRYE 353 (430)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~~~~h~~~~g~~~~C~~~~ 353 (430)
.||.|+.+++..+ .+.+|. .|+.. +|--|+.+...-..-...-|.|+.-.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~-~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE-ACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET-TT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT
T ss_pred cCCCCCCccEEeC--CEEECc-cccccceecccCCCcccHHHHHHHhcccceeeccCC
Confidence 6999999999888 789998 89854 69999888654332222457777643
No 93
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.05 E-value=0.91 Score=37.44 Aligned_cols=40 Identities=23% Similarity=0.546 Sum_probs=25.9
Q ss_pred eecCCCCCCceEEeecC------CCCceEEe-cCCCccccccCCcCCCC
Q 014105 231 KWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAHRP 272 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~~ 272 (430)
..|- +|...+...+. .......| .|+..||..|..-+|.-
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 4576 48765532211 12235679 99999999998777754
No 94
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.89 E-value=0.45 Score=47.12 Aligned_cols=50 Identities=30% Similarity=0.736 Sum_probs=35.2
Q ss_pred ccccccccccccCC-Ceeecc-CCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 141 EMTCGICFENYPSD-RLLAAA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 141 ~~~C~IC~e~~~~~-~~~~l~-CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
...|.||-+-++.. ++.... |||.|...|+.+|++..-.. -.|| .|+..+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~------R~cp--ic~ik~ 55 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN------RGCP--ICQIKL 55 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc------CCCC--ceeecc
Confidence 35699996656543 444455 99999999999999885543 2577 566433
No 95
>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=83.52 E-value=1 Score=36.55 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=26.6
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHH
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWT 171 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~ 171 (430)
...|++|...+....++..||||.|...|.+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4569999999877778888999999999975
No 96
>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=83.19 E-value=0.74 Score=44.86 Aligned_cols=53 Identities=26% Similarity=0.612 Sum_probs=31.9
Q ss_pred ecCCCCCCceEEeecCCCCceEEecCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCcceee
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEK 311 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~IeK 311 (430)
-||. |..-....+. ....+. .|||.||..|.... | .....+||.|+.++-|
T Consensus 5 ~CP~--Ck~~~y~np~-~kl~i~-~CGH~~C~sCv~~l------------------------~-~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPR--CKTTKYRNPS-LKLMVN-VCGHTLCESCVDLL------------------------F-VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCc--CCCCCccCcc-cccccC-CCCCcccHHHHHHH------------------------h-cCCCCCCCCCCCccch
Confidence 4885 8753322211 123344 89999999995221 1 1223689999999876
Q ss_pred cC
Q 014105 312 NQ 313 (430)
Q Consensus 312 ~~ 313 (430)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 53
No 97
>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=81.96 E-value=0.46 Score=31.20 Aligned_cols=32 Identities=28% Similarity=0.824 Sum_probs=22.0
Q ss_pred CCCCCcceeecCCCCceEecCCCccccccccccccccC
Q 014105 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (430)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (430)
||-|...+. +.+.-. .|||.||+.|...|...
T Consensus 1 C~iC~~~~~-----~~~~~~-~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELR-----DPVVVT-PCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-S-----SEEEEC-TTSEEEEHHHHHHHHHC
T ss_pred CCCCCCccc-----CcCEEC-CCCCchhHHHHHHHHHC
Confidence 556655554 244566 69999999999887544
No 98
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=81.61 E-value=2.3 Score=42.27 Aligned_cols=47 Identities=34% Similarity=0.783 Sum_probs=37.7
Q ss_pred ccccccccccccC--CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
.+.|..|.+.+.. +....+||.|.|...|+..|+.. .+ +-.|| .|+.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~----~rsCP--~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG----TRSCP--NCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC----CCCCc--cHHH
Confidence 6789999998764 45678999999999999999944 33 45899 7874
No 99
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.57 E-value=1.1 Score=42.93 Aligned_cols=28 Identities=29% Similarity=0.781 Sum_probs=22.6
Q ss_pred ccccccccccccCCCeeeccCCCc-ccHHHH
Q 014105 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCW 170 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl 170 (430)
...|.||++. +.+-+.|+|||. .|..|=
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhc
Confidence 5679999985 367889999995 687774
No 100
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.35 E-value=1.3 Score=30.33 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=20.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 329 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FC 329 (430)
-.||+|+..++...+=..++|. .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp-~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCP-YCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECC-CCCCeEE
Confidence 4699999988765443378887 7876553
No 101
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=81.17 E-value=1.3 Score=29.90 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=21.7
Q ss_pred HHHHhcCCCCCCCCcceeecCCCCceEecC-CCcccc
Q 014105 293 NWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFEF 328 (430)
Q Consensus 293 ~~i~~~tk~CP~C~~~IeK~~GCnhm~C~~-~C~~~F 328 (430)
.|.+...|.||+|++.- |+--+.|.. .|.+.|
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchhh
Confidence 45666789999999875 666666653 354443
No 102
>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=80.68 E-value=3 Score=46.53 Aligned_cols=20 Identities=10% Similarity=0.069 Sum_probs=13.6
Q ss_pred HHHHHHHhcCCChhhhhhhh
Q 014105 96 AASILLRFYNWSVSKVHDEW 115 (430)
Q Consensus 96 ~a~~LL~~~~W~~~~l~~~~ 115 (430)
.++..+.+|+-.+-.|++-|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56677777876666666654
No 103
>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=80.55 E-value=0.97 Score=29.47 Aligned_cols=27 Identities=26% Similarity=0.705 Sum_probs=17.7
Q ss_pred CCCCCCCcceeec------CCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKN------QGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~------~GCnhm~C~~~C~~~F 328 (430)
-.||+|+..+.-. .| ..+.|. .|++.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~-~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCG-KCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECC-CCCCEE
Confidence 3688888865522 22 378887 788765
No 104
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.36 E-value=1.5 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.670 Sum_probs=21.2
Q ss_pred eecCCCCCCceEEeecC---CCCceEEe-cCCCcc
Q 014105 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (430)
+.||+ |+..+.+... .+...|.| .|++.|
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57885 9988876543 34568999 898876
No 105
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.17 E-value=1.1 Score=46.61 Aligned_cols=37 Identities=27% Similarity=0.681 Sum_probs=31.0
Q ss_pred CCCCC--CCCcceee-cCCCCceEecCCCccccccccccccc
Q 014105 299 SKPCP--RCKRPIEK-NQGCMHMTCTPPCKFEFCWLCLGQWS 337 (430)
Q Consensus 299 tk~CP--~C~~~IeK-~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (430)
.|-|| .|+..+.- .+.+.-+.|. |++.|||.|+.+|.
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~--~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCG--CGHEFCFACGEESH 197 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCC--CCchhHhhcccccc
Confidence 35566 79998887 7889999997 99999999988774
No 106
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.13 E-value=1.5 Score=41.87 Aligned_cols=43 Identities=26% Similarity=0.819 Sum_probs=31.8
Q ss_pred cccccccccccCCCeeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 142 MTCGICFENYPSDRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
+.|+.|-..+ .++... .|+|.||.+|+..-+... .+.|| .|..
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds--------Df~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS--------DFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc--------cccCC--Cccc
Confidence 7899998654 444444 599999999998765541 57899 7775
No 107
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=79.37 E-value=1.6 Score=28.11 Aligned_cols=28 Identities=25% Similarity=0.664 Sum_probs=17.2
Q ss_pred CCCCCCCccee-ecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (430)
+-||.|+.++. +.++=.++.|+ .|++.+
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~-~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACR-TCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEES-SSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCC-CCCCcc
Confidence 57999998775 33333333898 798764
No 108
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.03 E-value=1.4 Score=41.15 Aligned_cols=53 Identities=13% Similarity=0.238 Sum_probs=38.8
Q ss_pred CccccccccccccCCCe--eeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 140 EEMTCGICFENYPSDRL--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
..+.|+||-+.+...-+ +.-+|||.||.+|...+|.. ...|| .|..++....|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~---------D~v~p--v~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK---------DMVDP--VTDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc---------ccccc--CCCCcCcccce
Confidence 57889999998854322 33479999999999999875 23577 67777765544
No 109
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=78.60 E-value=1.8 Score=27.76 Aligned_cols=27 Identities=33% Similarity=0.903 Sum_probs=15.1
Q ss_pred CCCCCCCcceeec----CCCCceEecCCCccc
Q 014105 300 KPCPRCKRPIEKN----QGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~IeK~----~GCnhm~C~~~C~~~ 327 (430)
|-||+|+.+++.. ++=.++.|. .||+-
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~-~Cg~I 31 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCP-ACGFI 31 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEET-TTTEE
T ss_pred CccccccChhhhhcCCCCCccceECC-CCCCE
Confidence 4699999999864 556678898 78763
No 110
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.56 E-value=0.64 Score=51.02 Aligned_cols=52 Identities=17% Similarity=0.524 Sum_probs=37.2
Q ss_pred CCccccccccccccC---CCe-eec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 139 GEEMTCGICFENYPS---DRL-LAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~---~~~-~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
+...+|+||+..+.. .-| ... .|.|.|...|+-.|+.+.- .-+|| .|+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~-------~s~CP--lCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA-------RSNCP--LCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC-------CCCCC--ccccccc
Confidence 456689999986541 111 122 4999999999999999843 24799 8987664
No 111
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=78.50 E-value=1.3 Score=42.59 Aligned_cols=40 Identities=23% Similarity=0.573 Sum_probs=31.4
Q ss_pred CCccccccccccccCCC-eeeccCCCcccHHHHHHHHHhhh
Q 014105 139 GEEMTCGICFENYPSDR-LLAAACGHPFCSSCWTGYISTAI 178 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~yi~~~i 178 (430)
.+...|.||+--|.... +..++|-|+|...|+.+|+....
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 34566888887776555 67788999999999999997543
No 112
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.32 E-value=1 Score=40.05 Aligned_cols=32 Identities=34% Similarity=0.977 Sum_probs=23.0
Q ss_pred EEecCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCccee
Q 014105 253 VTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (430)
Q Consensus 253 v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~Ie 310 (430)
|.=+||+.||..|.+. ...++.+||-|+..|-
T Consensus 147 vsTkCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 147 VSTKCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 4458999999998521 1234589999998664
No 113
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.17 E-value=1.9 Score=46.74 Aligned_cols=9 Identities=33% Similarity=1.202 Sum_probs=5.8
Q ss_pred eecCCCCCCce
Q 014105 231 KWCPAPGCDYA 241 (430)
Q Consensus 231 ~~CP~p~C~~~ 241 (430)
+.||. |+..
T Consensus 2 ~~Cp~--Cg~~ 10 (645)
T PRK14559 2 LICPQ--CQFE 10 (645)
T ss_pred CcCCC--CCCc
Confidence 46774 8764
No 114
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=77.64 E-value=0.98 Score=48.68 Aligned_cols=46 Identities=24% Similarity=0.659 Sum_probs=29.1
Q ss_pred CceecCCCCCCceEEeecCCCCce-EEecCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCc
Q 014105 229 KTKWCPAPGCDYAVDFVVGSGNYD-VTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKR 307 (430)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~~~-v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~ 307 (430)
.+..||. |.. .... |.=.|+|.||+.|-+. .+.+..++||+|+.
T Consensus 642 ~~LkCs~--Cn~--------R~Kd~vI~kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~ 686 (698)
T KOG0978|consen 642 ELLKCSV--CNT--------RWKDAVITKCGHVFCEECVQT-------------------------RYETRQRKCPKCNA 686 (698)
T ss_pred hceeCCC--ccC--------chhhHHHHhcchHHHHHHHHH-------------------------HHHHhcCCCCCCCC
Confidence 4578885 752 1122 2237999999999522 12223389999988
Q ss_pred ce
Q 014105 308 PI 309 (430)
Q Consensus 308 ~I 309 (430)
+.
T Consensus 687 aF 688 (698)
T KOG0978|consen 687 AF 688 (698)
T ss_pred CC
Confidence 76
No 115
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.61 E-value=1.8 Score=41.23 Aligned_cols=54 Identities=22% Similarity=0.567 Sum_probs=39.9
Q ss_pred CCccccccccccccCCCeeecc--CCCcccHHHHHHHHHhhhcCCCceeecccCC-CCCCC
Q 014105 139 GEEMTCGICFENYPSDRLLAAA--CGHPFCSSCWTGYISTAINDGPGCLMLRCPD-PSCGA 196 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~-~~C~~ 196 (430)
...+-|.+|-+.+...-++..+ =.|.||.-|-++.|+.+-..| .+.||. ..|..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg----evYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG----EVYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC----ceeCCCCCcCcc
Confidence 3468999999988544455444 379999999999999876655 577885 34654
No 116
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=76.93 E-value=5.2 Score=26.82 Aligned_cols=23 Identities=30% Similarity=1.042 Sum_probs=17.6
Q ss_pred CCCCCCCcceee-cCCCCceEecCCCc
Q 014105 300 KPCPRCKRPIEK-NQGCMHMTCTPPCK 325 (430)
Q Consensus 300 k~CP~C~~~IeK-~~GCnhm~C~~~C~ 325 (430)
..||.|+.|+-+ ..| .+.|. .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv-~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCV-SCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECC-CCC
Confidence 789999999987 455 57776 564
No 117
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=76.91 E-value=0.89 Score=41.24 Aligned_cols=31 Identities=29% Similarity=0.853 Sum_probs=23.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccccccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (430)
-.||-|...+. . -.-+ .|||.|||.|+..|.
T Consensus 19 ~~CpICld~~~-----d-PVvT-~CGH~FC~~CI~~wl 49 (193)
T PLN03208 19 FDCNICLDQVR-----D-PVVT-LCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCccCCCcCC-----C-cEEc-CCCchhHHHHHHHHH
Confidence 57999987664 1 2334 599999999999884
No 118
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=76.70 E-value=3.5 Score=40.28 Aligned_cols=77 Identities=26% Similarity=0.560 Sum_probs=48.4
Q ss_pred CCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcChHHHHHHHH
Q 014105 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~ 217 (430)
....++||||++.+. ..+++..=||..|..|-. ++ .-+|| .|+..++ .++.++- +
T Consensus 45 ~~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~-----~~-------~~~CP--~Cr~~~g--~~R~~am----E---- 99 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRT-----KV-------SNKCP--TCRLPIG--NIRCRAM----E---- 99 (299)
T ss_pred chhhccCchhhccCc-ccceecCCCcEehhhhhh-----hh-------cccCC--ccccccc--cHHHHHH----H----
Confidence 445789999999863 234444558999999986 11 45899 6998887 3333221 1
Q ss_pred HHHHHHHhcCCCceecCCC--CCCceEEee
Q 014105 218 YFIRSYVEDNRKTKWCPAP--GCDYAVDFV 245 (430)
Q Consensus 218 ~~~~~~v~~~~~~~~CP~p--~C~~~i~~~ 245 (430)
..++ ...+.||+. +|...+.+.
T Consensus 100 ----kV~e--~~~vpC~~~~~GC~~~~~Y~ 123 (299)
T KOG3002|consen 100 ----KVAE--AVLVPCKNAKLGCTKSFPYG 123 (299)
T ss_pred ----HHHH--hceecccccccCCceeeccc
Confidence 1111 234678864 787766554
No 119
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=76.54 E-value=0.72 Score=34.97 Aligned_cols=48 Identities=33% Similarity=0.753 Sum_probs=34.1
Q ss_pred ccccccccccC---------CC-eeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 143 TCGICFENYPS---------DR-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 143 ~C~IC~e~~~~---------~~-~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
+|+||.-.|.. ++ +..+ .|.|.|-.-|+.+++.+.-+++ .|| -|+..+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~------~CP--mcRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG------QCP--MCRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc------cCC--cchhee
Confidence 68888765532 22 2222 3999999999999999877765 588 687654
No 120
>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=76.03 E-value=1.6 Score=35.92 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=19.9
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
+.||+|++..---.- +.++|. .||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP-~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCP-KCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCC-CCCCcc
Confidence 689999987763222 889997 787765
No 121
>PLN03086 PRLI-interacting factor K; Provisional
Probab=75.32 E-value=4.9 Score=42.69 Aligned_cols=56 Identities=23% Similarity=0.543 Sum_probs=33.8
Q ss_pred ecccCCCCCCCCchhhHHHhhcChHHHHHHHHHHHHHHHhcCCCceecCCCCCCceEEeecCCCCceEEe-cCCCcc
Q 014105 186 MLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (430)
Q Consensus 186 ~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (430)
.+.|| .|...++...+...+. .-....+-||..+|+..+..... ...+.| .|+..|
T Consensus 407 ~V~C~--NC~~~i~l~~l~lHe~----------------~C~r~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f 463 (567)
T PLN03086 407 TVECR--NCKHYIPSRSIALHEA----------------YCSRHNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF 463 (567)
T ss_pred eEECC--CCCCccchhHHHHHHh----------------hCCCcceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence 67899 5998887655532111 11234578998789988754422 233567 676654
No 122
>PRK00420 hypothetical protein; Validated
Probab=75.21 E-value=5.1 Score=33.17 Aligned_cols=28 Identities=25% Similarity=0.248 Sum_probs=18.3
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCccccccccccc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (430)
....||.|+.++.+. +=|..||-.|+..
T Consensus 22 l~~~CP~Cg~pLf~l----------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 22 LSKHCPVCGLPLFEL----------KDGEVVCPVHGKV 49 (112)
T ss_pred ccCCCCCCCCcceec----------CCCceECCCCCCe
Confidence 348999999999741 1344555566653
No 123
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=74.78 E-value=2.2 Score=46.11 Aligned_cols=10 Identities=20% Similarity=0.259 Sum_probs=4.4
Q ss_pred cccchhhhcc
Q 014105 5 DEFDMQDANA 14 (430)
Q Consensus 5 ~~~~~~~~~~ 14 (430)
||.|+++.++
T Consensus 884 dd~d~~s~~~ 893 (988)
T KOG2038|consen 884 DDEDENSLGS 893 (988)
T ss_pred cccchhcccC
Confidence 3444444444
No 124
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=74.64 E-value=2.2 Score=34.03 Aligned_cols=30 Identities=23% Similarity=0.718 Sum_probs=22.7
Q ss_pred CCCCCCCccee--ecCCCCceEecCCCcccccc
Q 014105 300 KPCPRCKRPIE--KNQGCMHMTCTPPCKFEFCW 330 (430)
Q Consensus 300 k~CP~C~~~Ie--K~~GCnhm~C~~~C~~~FCw 330 (430)
..||.|+.++. +.+-||...|+ .|.+.|=-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~-tCpY~~~I 33 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCR-TCPYVFPI 33 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcC-CCCceeeE
Confidence 36999987654 44559999999 79987743
No 125
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=74.63 E-value=3.1 Score=26.79 Aligned_cols=27 Identities=22% Similarity=0.658 Sum_probs=17.5
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (430)
++||. |++.+....+..... .| .|++.
T Consensus 2 ~FCp~--C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCPE--CGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BETT--TTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCCC--CCccceEcCCCccCc-CCCCCCCc
Confidence 68985 999988765444333 78 77764
No 126
>PF04641 Rtf2: Rtf2 RING-finger
Probab=74.55 E-value=4 Score=39.15 Aligned_cols=59 Identities=17% Similarity=0.465 Sum_probs=42.2
Q ss_pred CCCccccccccccccC-CCeeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHHHhhcC
Q 014105 138 DGEEMTCGICFENYPS-DRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS 208 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~-~~~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i~~ll~ 208 (430)
....+.|||....+.. ..++.+ +|||+|+..+++..= .+ -.|| .|+..+....|-.|.+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~------~~Cp--~c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS------KKCP--VCGKPFTEEDIIPLNP 170 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc------cccc--ccCCccccCCEEEecC
Confidence 3567899999988853 244444 899999999999871 12 2599 8999987665544443
No 127
>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=74.07 E-value=4.7 Score=38.71 Aligned_cols=49 Identities=29% Similarity=0.646 Sum_probs=33.6
Q ss_pred ccccccccccC-CCeee--ccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhh
Q 014105 143 TCGICFENYPS-DRLLA--AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (430)
Q Consensus 143 ~C~IC~e~~~~-~~~~~--l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~ 201 (430)
.||+|-...-. -.++. -+|+|..|.+|+-..+.. | +-.|| .|..++...
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g----~~~Cp--eC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G----PAQCP--ECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C----CCCCC--cccchhhhc
Confidence 48888765321 12222 279999999999988865 3 34799 999887443
No 128
>PF12773 DZR: Double zinc ribbon
Probab=73.37 E-value=2.7 Score=29.12 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=8.6
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
+.||+|+..+.
T Consensus 30 ~~C~~Cg~~~~ 40 (50)
T PF12773_consen 30 KICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCCc
Confidence 67888888775
No 129
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=73.17 E-value=3 Score=29.50 Aligned_cols=28 Identities=29% Similarity=0.545 Sum_probs=16.7
Q ss_pred CCCCCCCccee------ecCCCCceE-ecCCCcccc
Q 014105 300 KPCPRCKRPIE------KNQGCMHMT-CTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~Ie------K~~GCnhm~-C~~~C~~~F 328 (430)
|+||.|+..-+ .+.+..++. |. .|++..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~-~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS-TCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC-CCCCCc
Confidence 89999986555 123444443 65 455543
No 130
>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=72.90 E-value=2.7 Score=31.30 Aligned_cols=29 Identities=38% Similarity=0.828 Sum_probs=21.1
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCccc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
.++.||.|+....+...=-.++|. .||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~-~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCP-NCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcC-CCCCE
Confidence 468999999999884444467776 56654
No 131
>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=72.84 E-value=4.6 Score=45.11 Aligned_cols=6 Identities=17% Similarity=0.108 Sum_probs=2.4
Q ss_pred HhHcCC
Q 014105 87 STVLSI 92 (430)
Q Consensus 87 ~~~l~i 92 (430)
+..|+.
T Consensus 709 ~~aL~~ 714 (784)
T PF04931_consen 709 AKALGD 714 (784)
T ss_pred HHHhcc
Confidence 333443
No 132
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.24 E-value=5.2 Score=43.85 Aligned_cols=41 Identities=24% Similarity=0.626 Sum_probs=31.1
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
-.|..|--.+. -.++...|||.|...|+. ++ .-.|| .|...
T Consensus 841 skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~----~~~CP--~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK----EDKCP--KCLPE 881 (933)
T ss_pred eeecccCCccc-cceeeeecccHHHHHhhc--------cC----cccCC--ccchh
Confidence 57999976653 245677899999999998 33 35899 88863
No 133
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=72.12 E-value=11 Score=24.22 Aligned_cols=32 Identities=25% Similarity=0.312 Sum_probs=26.5
Q ss_pred HHHHHHHhHcCCCHHHHHHHHHhcCCChhhhhh
Q 014105 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (430)
Q Consensus 81 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~ 113 (430)
+.|.++.+. |.+...++..|+..+||++..++
T Consensus 4 ~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 4 EKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 567777777 99999999999999999987654
No 134
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.88 E-value=4.8 Score=37.09 Aligned_cols=54 Identities=19% Similarity=0.402 Sum_probs=41.9
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..|.+|--.+...+.+.+.|-|.|...|+......--.... -...+|| .|...|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTA-PaGyqCP--~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTA-PAGYQCP--CCSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCC-CCcccCC--CCCCcc
Confidence 45999998888889999999999999999988765433221 1257899 888765
No 135
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=70.72 E-value=4.1 Score=26.37 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=20.3
Q ss_pred eecCCCCCCceEEeecC---CCCceEEe-cCCCcc
Q 014105 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (430)
+.||+ |+..+.+... .....|.| .|++.|
T Consensus 3 i~Cp~--C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN--CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC--CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 56885 9988776533 23467899 898875
No 136
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=70.60 E-value=0.82 Score=43.97 Aligned_cols=42 Identities=24% Similarity=0.468 Sum_probs=26.2
Q ss_pred CCCceecCCCCCCceEEeecC------CCCceEEe-cCCCccccccCCcCC
Q 014105 227 NRKTKWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAH 270 (430)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H 270 (430)
++....|-. |+..+...+. .......| .|...||..|..-.|
T Consensus 359 ~~ks~~Cf~--CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 359 NPKSTHCFV--CQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred CCCCcccee--ccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 344456654 7665543322 12345789 899999999976555
No 137
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=70.20 E-value=3.1 Score=28.84 Aligned_cols=26 Identities=23% Similarity=0.607 Sum_probs=16.7
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
+.||+|+--+.-..-=+...|. +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CG-kCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACG-KCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEec-cccc
Confidence 7899999544433223367787 7875
No 138
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=68.85 E-value=2.4 Score=41.41 Aligned_cols=53 Identities=26% Similarity=0.726 Sum_probs=38.0
Q ss_pred ccccccccccccC--CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
.-.||+|.+.... .+++..+||-..|+=||.. |...++ =+|| -|+.....+.|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~ln-------grcp--acrr~y~denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNLN-------GRCP--ACRRKYDDENV 68 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhcc-------CCCh--Hhhhhccccce
Confidence 3459999998654 4677788999999999964 444343 2799 79887655444
No 139
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=67.76 E-value=2.1 Score=30.50 Aligned_cols=44 Identities=27% Similarity=0.646 Sum_probs=29.5
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
..|-.|... ......++|||..|..||-.-= .=-|| -|...+..
T Consensus 8 ~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~r-----------YngCP--fC~~~~~~ 51 (55)
T PF14447_consen 8 QPCVFCGFV--GTKGTVLPCGHLICDNCFPGER-----------YNGCP--FCGTPFEF 51 (55)
T ss_pred eeEEEcccc--ccccccccccceeeccccChhh-----------ccCCC--CCCCcccC
Confidence 446666543 2456778999999999995321 22588 78887754
No 140
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.73 E-value=4 Score=38.20 Aligned_cols=38 Identities=13% Similarity=0.168 Sum_probs=31.9
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcC
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAIND 180 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~ 180 (430)
.--|++|+..+ .+++..+=||.||++||.+||..+-++
T Consensus 43 FdcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 43 FDCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred cceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 34588999876 788899999999999999999887543
No 141
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.34 E-value=1.9 Score=46.51 Aligned_cols=16 Identities=25% Similarity=0.652 Sum_probs=8.8
Q ss_pred cCCCcccHHHHHHHHH
Q 014105 160 ACGHPFCSSCWTGYIS 175 (430)
Q Consensus 160 ~CgH~fC~~Cl~~yi~ 175 (430)
.|+|.||..|+..|-.
T Consensus 143 ~c~H~FC~~Ci~sWsR 158 (1134)
T KOG0825|consen 143 HTAHYFCEECVGSWSR 158 (1134)
T ss_pred ccccccHHHHhhhhhh
Confidence 3555555555555543
No 142
>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=67.12 E-value=3.7 Score=33.36 Aligned_cols=25 Identities=28% Similarity=0.770 Sum_probs=19.4
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
+.||.|+.++...+ +.+.|. .|++.
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~-~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCP-SCGYE 25 (104)
T ss_pred CCCcccCcccccCC--CeEECc-CCCCc
Confidence 36999999997654 378898 78876
No 143
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=66.64 E-value=4.8 Score=31.48 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=23.1
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-.||.|+...-|..+=---.|+ .||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~-kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCR-KCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcC-CCCCee
Confidence 5899999999888887777887 677655
No 144
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=66.56 E-value=3.6 Score=45.56 Aligned_cols=27 Identities=33% Similarity=1.123 Sum_probs=23.9
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 329 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FC 329 (430)
..||.|+..+...+||. +|. .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~-~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH-SCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC-CCCCCCC
Confidence 36999999999999998 899 8998766
No 145
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=65.98 E-value=19 Score=23.08 Aligned_cols=34 Identities=18% Similarity=0.209 Sum_probs=26.5
Q ss_pred HHHHHHhHcCCCHHHHHHHHHhcCCChhhhhhhhh
Q 014105 82 DITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (430)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~ 116 (430)
.|.++.+ +|.+...+...|+..+||+++..+-++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3444444 589999999999999999998876543
No 146
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.45 E-value=4.4 Score=44.58 Aligned_cols=39 Identities=18% Similarity=0.416 Sum_probs=32.4
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHhhh
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAI 178 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i 178 (430)
+.-.|.+|.-.+-...++..+|||.|..+|+..++....
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHccc
Confidence 356799999887767777889999999999999887644
No 147
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.27 E-value=2 Score=45.40 Aligned_cols=36 Identities=22% Similarity=0.610 Sum_probs=28.4
Q ss_pred ccccccccccccC--CCeeeccCCCcccHHHHHHHHHh
Q 014105 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~ 176 (430)
.+.|+||+..|-. -.++++.|||..|+.|+......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 3569999877643 35789999999999999876654
No 148
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.00 E-value=5.5 Score=39.06 Aligned_cols=50 Identities=28% Similarity=0.620 Sum_probs=34.5
Q ss_pred CCCCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
.......|.||...+ .-...+||+|..|.-|-.+.-. +-. .-.|| .|+..
T Consensus 57 tDEen~~C~ICA~~~--TYs~~~PC~H~~CH~Ca~RlRA--LY~-----~K~C~--~CrTE 106 (493)
T COG5236 57 TDEENMNCQICAGST--TYSARYPCGHQICHACAVRLRA--LYM-----QKGCP--LCRTE 106 (493)
T ss_pred cccccceeEEecCCc--eEEEeccCCchHHHHHHHHHHH--HHh-----ccCCC--ccccc
Confidence 345678899998765 4456689999999999765432 211 23587 78764
No 149
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=63.93 E-value=5.9 Score=27.53 Aligned_cols=27 Identities=26% Similarity=0.755 Sum_probs=16.6
Q ss_pred ecCCCCCCceEEeecCCCCceEEe-cCCCc
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (430)
+||. |+..+............| .|++.
T Consensus 2 FCp~--Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPK--CGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCC--CCCccccccCCCCCEEECCcCCCe
Confidence 7884 998776553323245677 67753
No 150
>PHA02926 zinc finger-like protein; Provisional
Probab=63.84 E-value=3.8 Score=37.91 Aligned_cols=54 Identities=22% Similarity=0.502 Sum_probs=32.9
Q ss_pred cCCCCCCCCcce-eec-CCCCceEecCCCccccccccccccccCCCCCCCcccCCc
Q 014105 298 NSKPCPRCKRPI-EKN-QGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNR 351 (430)
Q Consensus 298 ~tk~CP~C~~~I-eK~-~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~~~C~~ 351 (430)
.-+.|+-|--.+ +|. .++...-=.+.|+|.||+.|...|......+|....|+.
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi 224 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCC
Confidence 347899998665 332 222111011269999999999999864333445556764
No 151
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=63.68 E-value=6.5 Score=33.35 Aligned_cols=52 Identities=27% Similarity=0.693 Sum_probs=38.8
Q ss_pred CCccccccccccccCCCeeec--cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPSDRLLAA--ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
..-.+|.||-+......+... -||=..|.-|....|...- ....|| .|+..+
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~------~ypvCP--vCkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN------LYPVCP--VCKTSF 131 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc------cCCCCC--cccccc
Confidence 367899999987543333222 2999999999999998854 246899 898766
No 152
>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=63.37 E-value=3.1 Score=29.28 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=14.3
Q ss_pred ceEEe-cCCCccccccCCcCCCCC
Q 014105 251 YDVTC-RCSYSFCWNCTEEAHRPV 273 (430)
Q Consensus 251 ~~v~C-~C~~~fC~~C~~~~H~~~ 273 (430)
....| .|+..||..|-.-.|..+
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 56789 899999999987777654
No 153
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.01 E-value=5.2 Score=33.96 Aligned_cols=24 Identities=33% Similarity=0.779 Sum_probs=18.9
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 333 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~ 333 (430)
.+-||.|+.|+.+ +-|..||-+|+
T Consensus 28 ~~hCp~Cg~PLF~-----------KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFR-----------KDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCccee-----------eCCeEECCCCC
Confidence 3789999999963 36777777887
No 154
>PHA02929 N1R/p28-like protein; Provisional
Probab=62.59 E-value=3.5 Score=38.92 Aligned_cols=53 Identities=23% Similarity=0.468 Sum_probs=30.6
Q ss_pred ceecCCCCCCceEEeecCC-CCceEEecCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCcc
Q 014105 230 TKWCPAPGCDYAVDFVVGS-GNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRP 308 (430)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~-~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~ 308 (430)
...||- |...+...+.. ....+.-.|++.||..|-..| + .. ...||-|+.+
T Consensus 174 ~~eC~I--Cle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~W------------l-------------~~-~~tCPlCR~~ 225 (238)
T PHA02929 174 DKECAI--CMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW------------K-------------KE-KNTCPVCRTP 225 (238)
T ss_pred CCCCcc--CCcccccCccccccceecCCCCCcccHHHHHHH------------H-------------hc-CCCCCCCCCE
Confidence 356875 76543211100 011244489999999996433 2 11 2589999988
Q ss_pred ee
Q 014105 309 IE 310 (430)
Q Consensus 309 Ie 310 (430)
+.
T Consensus 226 ~~ 227 (238)
T PHA02929 226 FI 227 (238)
T ss_pred ee
Confidence 75
No 155
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=62.50 E-value=7.2 Score=28.70 Aligned_cols=28 Identities=36% Similarity=0.777 Sum_probs=17.8
Q ss_pred cCCCCCCCCcceee---cCCCCceEecCCCcc
Q 014105 298 NSKPCPRCKRPIEK---NQGCMHMTCTPPCKF 326 (430)
Q Consensus 298 ~tk~CP~C~~~IeK---~~GCnhm~C~~~C~~ 326 (430)
+.|+||.|+..+.+ .+|=-...|. .|+.
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~-~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCN-GCES 35 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcC-CCCc
Confidence 45999999876653 3444445565 4555
No 156
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.82 E-value=2.3 Score=40.20 Aligned_cols=34 Identities=35% Similarity=0.783 Sum_probs=26.7
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccccccccc-cccCC
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ-WSDHG 340 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~-~~~h~ 340 (430)
.+|+-|-..++ --.|+ .|||-|||.|+-. |..-.
T Consensus 216 ~kC~lC~e~~~------~ps~t-~CgHlFC~~Cl~~~~t~~k 250 (271)
T COG5574 216 YKCFLCLEEPE------VPSCT-PCGHLFCLSCLLISWTKKK 250 (271)
T ss_pred cceeeeecccC------Ccccc-cccchhhHHHHHHHHHhhc
Confidence 67988877775 35678 7999999999987 76544
No 157
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=60.50 E-value=8.6 Score=23.41 Aligned_cols=21 Identities=24% Similarity=0.833 Sum_probs=14.1
Q ss_pred CCCCCCcceeecCCCCceEec
Q 014105 301 PCPRCKRPIEKNQGCMHMTCT 321 (430)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~ 321 (430)
.||.|+..+.+..|=-..+|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999888888886
No 158
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=60.43 E-value=6.6 Score=43.02 Aligned_cols=54 Identities=24% Similarity=0.568 Sum_probs=40.5
Q ss_pred CCccccccccccccCCC-eeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 139 GEEMTCGICFENYPSDR-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
...++|.||++.+.... +.+. .|-|.|-..|++.|....-..+. ..-+|| .|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~--~~WrCP--~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ--DGWRCP--ACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC--ccccCC--cccc
Confidence 35788999999886543 4444 49999999999999998555443 356899 6773
No 159
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=59.96 E-value=2.1 Score=41.73 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=22.7
Q ss_pred CCCCCCCcceee-cCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK-~~GCnhm~C~~~C~~~F 328 (430)
.+||+|+..|-+ .-.=|.+.|. .|+++|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCP-KCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCC-CCCCCe
Confidence 899999998864 3455778998 899988
No 160
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=59.46 E-value=9.3 Score=27.22 Aligned_cols=32 Identities=25% Similarity=0.916 Sum_probs=25.7
Q ss_pred cccccccccccc-CCCeeecc-CCCcccHHHHHH
Q 014105 141 EMTCGICFENYP-SDRLLAAA-CGHPFCSSCWTG 172 (430)
Q Consensus 141 ~~~C~IC~e~~~-~~~~~~l~-CgH~fC~~Cl~~ 172 (430)
...|++|-+.|. ..+++..+ ||-.+-++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 346999999985 46677765 999999999964
No 161
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=59.24 E-value=11 Score=38.41 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=8.8
Q ss_pred CCCCCccccccccccc
Q 014105 136 FPDGEEMTCGICFENY 151 (430)
Q Consensus 136 ~~~~~~~~C~IC~e~~ 151 (430)
.|.+..|.|+-=-+.-
T Consensus 189 LPDSTDFVCGTLDEDR 204 (458)
T PF10446_consen 189 LPDSTDFVCGTLDEDR 204 (458)
T ss_pred CCCcccccCCCcCCcc
Confidence 4556667766544433
No 162
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=58.91 E-value=7.6 Score=25.64 Aligned_cols=31 Identities=23% Similarity=0.580 Sum_probs=25.2
Q ss_pred CCCCCCCcc-eeecCCCCceEecCCCccccccccccccccCC
Q 014105 300 KPCPRCKRP-IEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 300 k~CP~C~~~-IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
..|+.|... +. ++|. .|+..+|..|...- |.
T Consensus 4 ~~C~~H~~~~~~-------~~C~-~C~~~~C~~C~~~~--H~ 35 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCE-DCNEPLCSECTVSG--HK 35 (42)
T ss_dssp SB-SSTTTSBEE-------EEET-TTTEEEEHHHHHTS--TT
T ss_pred ccCccCCccceE-------EEec-CCCCccCccCCCCC--CC
Confidence 689999877 77 9999 89999999998643 64
No 163
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=58.88 E-value=33 Score=25.30 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhHcCCCHHHHHHHHHhcCCChhhhhhhhh
Q 014105 76 RQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (430)
Q Consensus 76 ~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~ 116 (430)
...+.+.|..++...+++..-+..+|...+||.+..+..|.
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34678889999999999999999999999999998887663
No 164
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=58.61 E-value=11 Score=26.45 Aligned_cols=36 Identities=14% Similarity=0.174 Sum_probs=30.4
Q ss_pred HHHHHHHhHcCCCHHHHHHHHHhcCCChhhhhhhhh
Q 014105 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (430)
Q Consensus 81 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~ 116 (430)
+.|..++...++++.-+...|...+||.++.+..|.
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 568899999999999999999999999998887664
No 165
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=58.50 E-value=7 Score=27.00 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=20.2
Q ss_pred CCCCC--CCCcceeecCCCCceEecCCCcc
Q 014105 299 SKPCP--RCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 299 tk~CP--~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
-+.|| .|+.-|.-..--+..+|. +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CG-KCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCG-KCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEET-TTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCC-Cccc
Confidence 37899 999987666666889999 7985
No 166
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=57.79 E-value=7.5 Score=37.41 Aligned_cols=47 Identities=30% Similarity=0.613 Sum_probs=36.2
Q ss_pred CCccccccccccccC--CCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 139 GEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
.....||||.+.+.. ..+..++|||..-..|++.++.. ..+|| .|..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~---------~y~CP--~C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE---------GYTCP--ICSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc---------CCCCC--cccc
Confidence 345669999987543 34566789999999999998876 26899 7887
No 167
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=56.85 E-value=8.9 Score=31.83 Aligned_cols=28 Identities=21% Similarity=0.645 Sum_probs=20.6
Q ss_pred CCCCCCCcceee--cCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK--~~GCnhm~C~~~C~~~F 328 (430)
+.||+|+.++.- .++=+-+.|+ +||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~-kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCR-KCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECC-CCCcch
Confidence 789999988874 2222388998 788875
No 168
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=56.40 E-value=32 Score=21.83 Aligned_cols=31 Identities=23% Similarity=0.225 Sum_probs=24.0
Q ss_pred HHHHHhHcCCCHHHHHHHHHhcCCChhhhhhh
Q 014105 83 ITRISTVLSISKVAASILLRFYNWSVSKVHDE 114 (430)
Q Consensus 83 i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~ 114 (430)
|+++.+ +|.+...++..|+..+||+++..+-
T Consensus 5 v~~L~~-mGf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 5 IDQLLE-MGFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHH
Confidence 344433 4899999999999999998887653
No 169
>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=56.17 E-value=7 Score=32.89 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=19.4
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
+.||+|++..---.- +.++|. .||..|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP-~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSP-YTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCC-CcCCcc
Confidence 789999987753222 778897 777663
No 170
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=55.93 E-value=8.7 Score=36.97 Aligned_cols=26 Identities=42% Similarity=0.954 Sum_probs=22.1
Q ss_pred CCCCCCCCcceeec--CCCCceEecCCCc
Q 014105 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (430)
Q Consensus 299 tk~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (430)
.++|+.|+.+|+|. +|=+-.+|. .|.
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP-~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCP-VCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCC-CCC
Confidence 47999999999965 888888887 786
No 171
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=55.45 E-value=11 Score=38.37 Aligned_cols=9 Identities=44% Similarity=0.545 Sum_probs=3.9
Q ss_pred HHHHHHHHH
Q 014105 364 SEKRREMAK 372 (430)
Q Consensus 364 ~~~~~~~~~ 372 (430)
.|+++++-|
T Consensus 395 LEkKRQrRK 403 (458)
T PF10446_consen 395 LEKKRQRRK 403 (458)
T ss_pred hhhhhhhhh
Confidence 344444433
No 172
>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=55.12 E-value=11 Score=26.34 Aligned_cols=47 Identities=17% Similarity=0.521 Sum_probs=24.5
Q ss_pred cccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
+.|+|-+..+. .......|.|.-|.+ +..|+....+.+ ..+|| .|+.
T Consensus 3 L~CPls~~~i~-~P~Rg~~C~H~~CFD-l~~fl~~~~~~~----~W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR-IPVRGKNCKHLQCFD-LESFLESNQRTP----KWKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-S-SEEEETT--SS--EE-HHHHHHHHHHS-------B-T--TT--
T ss_pred eeCCCCCCEEE-eCccCCcCcccceEC-HHHHHHHhhccC----CeECc--CCcC
Confidence 56888887652 234556799998876 677888777654 47899 7764
No 173
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=54.45 E-value=9.9 Score=30.76 Aligned_cols=28 Identities=25% Similarity=0.546 Sum_probs=17.9
Q ss_pred CCCCCCCCccee---ecCCCCceEecCCCccc
Q 014105 299 SKPCPRCKRPIE---KNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 299 tk~CP~C~~~Ie---K~~GCnhm~C~~~C~~~ 327 (430)
.-.||+|+.... +..|=-|..|. .||+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~-~CG~y 51 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCG-NCGLY 51 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECC-CCCCc
Confidence 357999994322 33356688887 67665
No 174
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.32 E-value=7.2 Score=38.60 Aligned_cols=44 Identities=23% Similarity=0.664 Sum_probs=30.3
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
+....|.||.+.. .+.+.++|||.-| |..-+ .+ ...|| .|+..|
T Consensus 303 ~~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs--~~--------l~~CP--vCR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCS--KH--------LPQCP--VCRQRI 346 (355)
T ss_pred CCCCceEEecCCc--cceeeecCCcEEE--chHHH--hh--------CCCCc--hhHHHH
Confidence 3456799999875 5688899999966 54322 11 23599 787654
No 175
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=53.86 E-value=2.9 Score=40.72 Aligned_cols=28 Identities=18% Similarity=0.418 Sum_probs=17.7
Q ss_pred CCCCCCCcceeec-CCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~-~GCnhm~C~~~C~~~F 328 (430)
.+||+|+..|-+. -.=|...|. .|+++|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp-~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICE-QCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCC-CCCCCc
Confidence 6677777766533 345566776 677765
No 176
>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=53.67 E-value=8.8 Score=23.52 Aligned_cols=25 Identities=36% Similarity=0.806 Sum_probs=14.2
Q ss_pred CCCCCCCcceeec--CCCCceEecCCCc
Q 014105 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (430)
Q Consensus 300 k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (430)
++||.|+..|++. +|=+...|. .|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~-rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP-RCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T-TTC
T ss_pred CcCccCCCcceEeEecCCCCeECc-CCc
Confidence 6899999999753 555566665 554
No 177
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.55 E-value=10 Score=42.57 Aligned_cols=32 Identities=25% Similarity=0.599 Sum_probs=20.4
Q ss_pred CCCceecCCCCCCceEEeecCCCCceEEe-cCCC-----ccccccCCc
Q 014105 227 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSY-----SFCWNCTEE 268 (430)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~-----~fC~~C~~~ 268 (430)
....+.||. |+... ....| .||. .||..|+..
T Consensus 623 EVg~RfCps--CG~~t--------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 623 EIGRRKCPS--CGKET--------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred cccCccCCC--CCCcC--------CcccCCCCCCCCCcceeCccccCc
Confidence 345678985 88642 44678 6875 477777533
No 178
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=53.34 E-value=2.7 Score=29.16 Aligned_cols=33 Identities=30% Similarity=0.838 Sum_probs=27.2
Q ss_pred CccccccccccccCCCeeec-cCCCcccHHHHHH
Q 014105 140 EEMTCGICFENYPSDRLLAA-ACGHPFCSSCWTG 172 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~ 172 (430)
..++|.+|-..++...+... -||.--|..||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 36889999998887766654 4999999999985
No 179
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.10 E-value=13 Score=42.87 Aligned_cols=29 Identities=31% Similarity=0.924 Sum_probs=17.0
Q ss_pred ceecCCCCCCceEEeecCCCCceEEe-cCCCcc-----ccccCCc
Q 014105 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF-----CWNCTEE 268 (430)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f-----C~~C~~~ 268 (430)
.+.||. |+..+ +...| .||..+ |..|+..
T Consensus 667 ~rkCPk--CG~~t--------~~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCPS--CGTET--------YENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEECCC--CCCcc--------ccccCcccCCcCCCceeCccCCCc
Confidence 378884 87632 12367 677554 6666643
No 180
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=52.96 E-value=11 Score=28.93 Aligned_cols=59 Identities=24% Similarity=0.674 Sum_probs=19.8
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCcce
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~I 309 (430)
..|-. |+--|-.. ..+...|-| .|++..|..|. ++. ++..++-||+|+++.
T Consensus 10 qiCqi--CGD~VGl~-~~Ge~FVAC~eC~fPvCr~Cy----------EYE---------------rkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 10 QICQI--CGDDVGLT-ENGEVFVACHECAFPVCRPCY----------EYE---------------RKEGNQVCPQCKTRY 61 (80)
T ss_dssp -B-SS--S--B--B--SSSSB--S-SSS-----HHHH----------HHH---------------HHTS-SB-TTT--B-
T ss_pred ccccc--ccCccccC-CCCCEEEEEcccCCccchhHH----------HHH---------------hhcCcccccccCCCc
Confidence 34553 76655544 345677889 89998887663 221 223458999999998
Q ss_pred eecCCCCc
Q 014105 310 EKNQGCMH 317 (430)
Q Consensus 310 eK~~GCnh 317 (430)
.+..|+-.
T Consensus 62 kr~kgsp~ 69 (80)
T PF14569_consen 62 KRHKGSPR 69 (80)
T ss_dssp ---TT---
T ss_pred ccccCCCC
Confidence 87777654
No 181
>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=52.73 E-value=11 Score=30.86 Aligned_cols=27 Identities=30% Similarity=0.994 Sum_probs=18.4
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-+||+|+...-=..|=+ +.|. .|+++|
T Consensus 3 p~CP~C~seytY~dg~~-~iCp-eC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP-SCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc-cccccc
Confidence 57999988776555544 6776 566654
No 182
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.70 E-value=47 Score=25.48 Aligned_cols=35 Identities=31% Similarity=0.779 Sum_probs=25.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccccccccccccCCC
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 341 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~ 341 (430)
..||.|++.+. |.=+..=-...|-.|.+.|-+-|.
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWLDrGE 36 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWLDRGE 36 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEeecchh
Confidence 56999999887 555423445678899999987663
No 183
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=52.41 E-value=14 Score=29.60 Aligned_cols=27 Identities=26% Similarity=0.768 Sum_probs=17.2
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCC
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSY 259 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~ 259 (430)
.+||. |++.+.+..+.....+.| .|.+
T Consensus 2 ~FCP~--Cgn~Live~g~~~~rf~C~tCpY 29 (105)
T KOG2906|consen 2 LFCPT--CGNMLIVESGESCNRFSCRTCPY 29 (105)
T ss_pred cccCC--CCCEEEEecCCeEeeEEcCCCCc
Confidence 47985 999888775443355555 5544
No 184
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=52.26 E-value=3.3 Score=40.22 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=21.6
Q ss_pred CCCCCCCcceeec-CCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~-~GCnhm~C~~~C~~~F 328 (430)
.+||+|+..|-+. -.=|.+.|. .|+++|
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCP-KCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCC-CCCCcC
Confidence 7899999888753 445668887 798876
No 185
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.03 E-value=61 Score=30.64 Aligned_cols=17 Identities=24% Similarity=0.608 Sum_probs=15.5
Q ss_pred CceEecCCCccccccccc
Q 014105 316 MHMTCTPPCKFEFCWLCL 333 (430)
Q Consensus 316 nhm~C~~~C~~~FCw~C~ 333 (430)
.++.|. .|....|+.|.
T Consensus 96 ~~~~c~-~~~~~~c~~c~ 112 (386)
T KOG2177|consen 96 LKLFCE-EDEKLLCVLCR 112 (386)
T ss_pred ceEEec-ccccccCCCCC
Confidence 569999 89999999997
No 186
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=51.77 E-value=12 Score=25.70 Aligned_cols=33 Identities=30% Similarity=0.615 Sum_probs=22.9
Q ss_pred cccccccccCCCeeeccCCC-----cccHHHHHHHHHh
Q 014105 144 CGICFENYPSDRLLAAACGH-----PFCSSCWTGYIST 176 (430)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH-----~fC~~Cl~~yi~~ 176 (430)
|-||++.-....+...||+- .....|+..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 67999886655556667653 5788999999988
No 187
>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=51.64 E-value=23 Score=31.06 Aligned_cols=84 Identities=24% Similarity=0.550 Sum_probs=46.7
Q ss_pred ccccccccccccCCCeeecc-------CCCccc------HHHHHHHHHhhhcCC----------------------Ccee
Q 014105 141 EMTCGICFENYPSDRLLAAA-------CGHPFC------SSCWTGYISTAINDG----------------------PGCL 185 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~-------CgH~fC------~~Cl~~yi~~~i~~g----------------------~~~~ 185 (430)
..+||||++. |. +-|.|- |.-+.| ..||.+|-....... ....
T Consensus 2 d~~CpICme~-PH-NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (162)
T PF07800_consen 2 DVTCPICMEH-PH-NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQP 79 (162)
T ss_pred CccCceeccC-CC-ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccc
Confidence 4689999974 43 334443 433344 478888876543221 1123
Q ss_pred ecccCCCCCCCCchhhHHHhhcChHHHHHHHHHHHHHHHhcCCCceecCCCCCCceEE
Q 014105 186 MLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVD 243 (430)
Q Consensus 186 ~i~CP~~~C~~~l~~~~i~~ll~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~ 243 (430)
.+.|| .|+..|.--.|- +- .+.|++ .+.+-|+.-+|.+...
T Consensus 80 ~L~CP--LCRG~V~GWtvv-----e~--------AR~~LN--~K~RsC~~e~C~F~Gt 120 (162)
T PF07800_consen 80 ELACP--LCRGEVKGWTVV-----EP--------ARRFLN--AKKRSCSQESCSFSGT 120 (162)
T ss_pred cccCc--cccCceeceEEc-----hH--------HHHHhc--cCCccCcccccccccC
Confidence 67898 788765332211 11 123333 3456899889987543
No 188
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=51.53 E-value=6.2 Score=31.70 Aligned_cols=32 Identities=31% Similarity=0.752 Sum_probs=24.5
Q ss_pred CCCccccccccccccCCCeeeccCCCcccHHH
Q 014105 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSC 169 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 169 (430)
...+|+|.-||=....+.+....=|+.+|++|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 35689999999776555655555689999998
No 189
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=51.00 E-value=13 Score=26.52 Aligned_cols=43 Identities=30% Similarity=0.828 Sum_probs=30.7
Q ss_pred ccccccccccCCCeeeccCCC--cccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 143 TCGICFENYPSDRLLAAACGH--PFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH--~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.|..|-.+++.+..-..-|.+ .||.+|....+.. .|| .|+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~-----------~CP--NCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG-----------VCP--NCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC-----------cCc--CCCCcc
Confidence 588898888766544444553 6999999877632 588 788765
No 190
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=50.86 E-value=15 Score=23.29 Aligned_cols=28 Identities=21% Similarity=0.284 Sum_probs=16.4
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
.+.|+.|+....-+.-=..+.|. .|+..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~-~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCI-FCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcc-cCCcE
Confidence 37899998777643333345555 45543
No 191
>PRK11827 hypothetical protein; Provisional
Probab=50.71 E-value=14 Score=26.97 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=19.7
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
-.||.|+..++-..+=+...|. .|+-.
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~-~~~la 35 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICK-LDNLA 35 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECC-ccCee
Confidence 5799999999866555667787 55543
No 192
>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=50.55 E-value=20 Score=23.96 Aligned_cols=12 Identities=33% Similarity=1.146 Sum_probs=9.0
Q ss_pred CCCCCCCc-ceee
Q 014105 300 KPCPRCKR-PIEK 311 (430)
Q Consensus 300 k~CP~C~~-~IeK 311 (430)
..||.|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 67888887 6654
No 193
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=50.28 E-value=24 Score=27.08 Aligned_cols=50 Identities=24% Similarity=0.627 Sum_probs=19.8
Q ss_pred CCccccccccccccCC---Cee-ec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPSD---RLL-AA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~---~~~-~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.....|.||-+.+... +++ .. .|+-..|+.|+.--. ++|. -.|| .|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~----q~Cp--qCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGN----QVCP--QCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS-----SB-T--TT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCc----cccc--ccCCCc
Confidence 4456899999987542 333 33 489999999986443 3453 4698 788654
No 194
>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=49.66 E-value=19 Score=24.08 Aligned_cols=24 Identities=25% Similarity=0.653 Sum_probs=11.9
Q ss_pred CCCCCCcc-eeecCCCCceEecCCCc
Q 014105 301 PCPRCKRP-IEKNQGCMHMTCTPPCK 325 (430)
Q Consensus 301 ~CP~C~~~-IeK~~GCnhm~C~~~C~ 325 (430)
.||.|+.. |.-+..=.-+.|+ .||
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~-~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCP-NCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEET-TT-
T ss_pred CCcCCcCCceEEcCCCCeEECC-CCC
Confidence 48888765 3333333334555 444
No 195
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=49.64 E-value=19 Score=35.04 Aligned_cols=51 Identities=20% Similarity=0.445 Sum_probs=34.3
Q ss_pred Ccccccccccccc-CCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 140 EEMTCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 140 ~~~~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
+-|+||+=-+.-. .+.|+.+.|||.+=+.=+...- ++| ...++|| -|+..-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG--~~~FKCP--YCP~~~ 386 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNG--VLSFKCP--YCPEMS 386 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcC--cEEeeCC--CCCcch
Confidence 4689998554433 3567899999998776554332 234 3589999 787643
No 196
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=49.56 E-value=7.2 Score=28.18 Aligned_cols=40 Identities=33% Similarity=0.528 Sum_probs=30.8
Q ss_pred CCCCCCCcceee--cCCCCceEecCCCccccccccccccccCC
Q 014105 300 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 300 k~CP~C~~~IeK--~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
..||-|+...-- .+-=|+-+|+ .|+...|-+||-.-.+|-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT-~Ck~~VCnlCGFNP~Phl 44 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCT-ECKSQVCNLCGFNPTPHL 44 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHH-HHhhhhhcccCCCCCccc
Confidence 579999887731 1346899999 899999999986555554
No 197
>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=49.49 E-value=16 Score=24.69 Aligned_cols=34 Identities=18% Similarity=0.478 Sum_probs=16.9
Q ss_pred cccccccccCCCeee-ccCCCcccHHHHHHHHHhh
Q 014105 144 CGICFENYPSDRLLA-AACGHPFCSSCWTGYISTA 177 (430)
Q Consensus 144 C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~yi~~~ 177 (430)
|.+|-+.......-. ..|+=.+-..|+..||...
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~ 35 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR 35 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC
Confidence 667766543222211 2488889999999999874
No 198
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=48.96 E-value=11 Score=40.92 Aligned_cols=7 Identities=43% Similarity=0.781 Sum_probs=2.6
Q ss_pred Cccccch
Q 014105 3 SEDEFDM 9 (430)
Q Consensus 3 ~~~~~~~ 9 (430)
+|+|.++
T Consensus 874 ~D~d~~~ 880 (988)
T KOG2038|consen 874 SDDDVDA 880 (988)
T ss_pred ccccccc
Confidence 3333344
No 199
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=48.93 E-value=54 Score=37.00 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=9.8
Q ss_pred CcccEE---ecHHHHHHHHH
Q 014105 64 QLNYTV---LTEADIRQRQE 80 (430)
Q Consensus 64 ~~~~~~---l~~~~i~~~~~ 80 (430)
+..|++ -|.+++...+.
T Consensus 417 elPftf~~P~s~eel~~lL~ 436 (840)
T PF04147_consen 417 ELPFTFPCPSSHEELLELLD 436 (840)
T ss_pred CCCceecCCCCHHHHHHHHh
Confidence 456764 46677655543
No 200
>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=48.49 E-value=15 Score=27.15 Aligned_cols=35 Identities=20% Similarity=0.399 Sum_probs=19.6
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCcccccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~ 336 (430)
+..|+.|++..- ---..-.|+ .||..||-.|....
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr-~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCR-NCGRVVCSSCSSQR 43 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-T-TT--EEECCCS-EE
T ss_pred CCcCcCcCCcCC--CceeeEccC-CCCCEECCchhCCE
Confidence 488999999883 335567899 89999999998654
No 201
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.32 E-value=14 Score=35.63 Aligned_cols=27 Identities=44% Similarity=0.942 Sum_probs=19.6
Q ss_pred CCCCCCCCcceee--cCCCCceEecCCCcc
Q 014105 299 SKPCPRCKRPIEK--NQGCMHMTCTPPCKF 326 (430)
Q Consensus 299 tk~CP~C~~~IeK--~~GCnhm~C~~~C~~ 326 (430)
.++||.|+.+|+| .+|=.-.+|. .|+.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp-~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP-QCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC-CCcC
Confidence 3799999999985 3676666665 5653
No 202
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.04 E-value=12 Score=24.75 Aligned_cols=32 Identities=31% Similarity=0.687 Sum_probs=19.4
Q ss_pred CCCCCCcceeecCCCCceEecCCCccccccccccccccC
Q 014105 301 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (430)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (430)
.||+|+..++...- . .=...-|-.|++.|-+.
T Consensus 1 ~CP~C~~~l~~~~~-~------~~~id~C~~C~G~W~d~ 32 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-G------DVEIDVCPSCGGIWFDA 32 (41)
T ss_pred CcCCCCcccceEEE-C------CEEEEECCCCCeEEccH
Confidence 59999998874433 1 12233456777777643
No 203
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.72 E-value=13 Score=26.89 Aligned_cols=23 Identities=30% Similarity=0.846 Sum_probs=17.1
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCcc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
+.-.||.|+.+.. .|-.|. .||+
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~-~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCP-SCGY 48 (57)
T ss_pred cceECCCCCCccC-----CeEECC-CCCc
Confidence 4468999999987 577776 5664
No 204
>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=46.56 E-value=20 Score=33.91 Aligned_cols=20 Identities=20% Similarity=0.566 Sum_probs=15.7
Q ss_pred CCceecCCCCCCceEEeecC
Q 014105 228 RKTKWCPAPGCDYAVDFVVG 247 (430)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~ 247 (430)
...+-||+|+|..+|...+.
T Consensus 121 S~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred cccccCCCCCCcceEEeCCc
Confidence 34578999999999977543
No 205
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.24 E-value=17 Score=40.12 Aligned_cols=36 Identities=22% Similarity=0.695 Sum_probs=29.7
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccc-----cccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (430)
+-.||+|..++.-...=|.|.|. .||++ .|..|+..
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 34789998888766666999999 89988 89999976
No 206
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=44.99 E-value=4.5 Score=29.40 Aligned_cols=11 Identities=55% Similarity=1.313 Sum_probs=9.2
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
|-||.||.+|.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 67888888886
No 207
>PF14149 YhfH: YhfH-like protein
Probab=44.99 E-value=1.7 Score=28.27 Aligned_cols=25 Identities=32% Similarity=0.877 Sum_probs=20.6
Q ss_pred CCCCCCCCcceeecCCCCceEecCCC
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPC 324 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C 324 (430)
.|.||.||..|+--.-|..++|. .|
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~C~-~C 37 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNECD-RC 37 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCcCC-CC
Confidence 59999999999877777777776 55
No 208
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=44.84 E-value=17 Score=35.12 Aligned_cols=26 Identities=42% Similarity=0.962 Sum_probs=19.6
Q ss_pred CCCCCCCCcceeec--CCCCceEecCCCc
Q 014105 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (430)
Q Consensus 299 tk~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (430)
.++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCP-RCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECc-CCC
Confidence 37999999999864 676666676 565
No 209
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=44.49 E-value=7 Score=37.38 Aligned_cols=29 Identities=17% Similarity=0.504 Sum_probs=23.4
Q ss_pred CCCCCCCcceee-cCCCCceEecCCCccccc
Q 014105 300 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEFC 329 (430)
Q Consensus 300 k~CP~C~~~IeK-~~GCnhm~C~~~C~~~FC 329 (430)
.+||+|+..+-+ .-+=|...|. +|+++|=
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp-~c~~h~r 58 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCP-KCGHHMR 58 (294)
T ss_pred eECCCccceeeHHHHHhhhhccc-ccCcccc
Confidence 789999998875 4577888897 7888773
No 210
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=44.34 E-value=18 Score=23.13 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=22.6
Q ss_pred CCCCCCc-ceeecCCCCceEecCCCcccccccccc
Q 014105 301 PCPRCKR-PIEKNQGCMHMTCTPPCKFEFCWLCLG 334 (430)
Q Consensus 301 ~CP~C~~-~IeK~~GCnhm~C~~~C~~~FCw~C~~ 334 (430)
.||.|+. ++. ++|. .|+...|..|..
T Consensus 2 ~C~~H~~~~~~-------~fC~-~~~~~iC~~C~~ 28 (39)
T cd00021 2 LCDEHGEEPLS-------LFCE-TDRALLCVDCDL 28 (39)
T ss_pred CCCccCCcceE-------EEeC-ccChhhhhhcCh
Confidence 5888877 877 9999 899999999964
No 211
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.13 E-value=18 Score=34.95 Aligned_cols=26 Identities=42% Similarity=0.907 Sum_probs=19.6
Q ss_pred CCCCCCCCcceeec--CCCCceEecCCCc
Q 014105 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (430)
Q Consensus 299 tk~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (430)
.++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCP-QCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECC-CCC
Confidence 36999999999864 776667776 563
No 212
>PRK10220 hypothetical protein; Provisional
Probab=44.06 E-value=18 Score=29.56 Aligned_cols=27 Identities=26% Similarity=0.763 Sum_probs=17.7
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-+||+|....-=..|=+ +.|. .|+++|
T Consensus 4 P~CP~C~seytY~d~~~-~vCp-eC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICP-ECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECC-cccCcC
Confidence 58999987765555533 6676 566654
No 213
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.99 E-value=17 Score=35.02 Aligned_cols=26 Identities=35% Similarity=0.879 Sum_probs=19.6
Q ss_pred CCCCCCCCcceee--cCCCCceEecCCCc
Q 014105 299 SKPCPRCKRPIEK--NQGCMHMTCTPPCK 325 (430)
Q Consensus 299 tk~CP~C~~~IeK--~~GCnhm~C~~~C~ 325 (430)
.++||.|+.+|++ .+|=.-.+|. .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP-~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCP-HCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECc-CCc
Confidence 4799999999985 4776666665 564
No 214
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=43.46 E-value=76 Score=20.92 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=28.5
Q ss_pred HHHHHHHhHc-CCCHHHHHHHHHhcCCChhhhhhhhhh
Q 014105 81 EDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWFA 117 (430)
Q Consensus 81 ~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~~~~~~ 117 (430)
+.|..+.+++ ++++......|+.+++|++..++....
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4566666666 578889999999999999998887654
No 215
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=43.42 E-value=14 Score=42.52 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=22.7
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc-----cccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF-----CWLCLGQW 336 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F-----Cw~C~~~~ 336 (430)
++||+|+..+.. -+|. .||... |-.|+...
T Consensus 668 rkCPkCG~~t~~------~fCP-~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCP-DCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCc-ccCCcCCCceeCccCCCcc
Confidence 789999998743 2887 788664 88888754
No 216
>PRK10445 endonuclease VIII; Provisional
Probab=43.05 E-value=18 Score=34.63 Aligned_cols=25 Identities=32% Similarity=0.627 Sum_probs=19.7
Q ss_pred CCCCCCCcceee--cCCCCceEecCCCc
Q 014105 300 KPCPRCKRPIEK--NQGCMHMTCTPPCK 325 (430)
Q Consensus 300 k~CP~C~~~IeK--~~GCnhm~C~~~C~ 325 (430)
++||.|+.+|++ .+|=.-.+|. .|+
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP-~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCP-GCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECC-CCc
Confidence 799999999985 4776667776 664
No 217
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.69 E-value=19 Score=34.98 Aligned_cols=26 Identities=38% Similarity=0.910 Sum_probs=20.4
Q ss_pred CCCCCCCCcceee--cCCCCceEecCCCc
Q 014105 299 SKPCPRCKRPIEK--NQGCMHMTCTPPCK 325 (430)
Q Consensus 299 tk~CP~C~~~IeK--~~GCnhm~C~~~C~ 325 (430)
.++||.|+.+|+| .+|=.-.+|. .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCP-NCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECC-CCc
Confidence 3799999999986 4777777776 665
No 218
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=42.54 E-value=8 Score=37.10 Aligned_cols=29 Identities=31% Similarity=0.881 Sum_probs=22.8
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (430)
-+|--|.-.|- +-|...|||.||++|-..
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~ 54 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRR 54 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHH
Confidence 57888887776 777447999999999764
No 219
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.17 E-value=8.4 Score=39.19 Aligned_cols=32 Identities=28% Similarity=0.685 Sum_probs=24.1
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccccccccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (430)
-.||-|...+. +.+. . .|+|.||..|...|..
T Consensus 27 l~C~IC~d~~~-----~Pvi-t-pCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-T-SCSHTFCSLCIRRCLS 58 (397)
T ss_pred cCCCcCchhhh-----CccC-C-CCCCchhHHHHHHHHh
Confidence 58999987764 3343 4 6999999999987653
No 220
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=42.10 E-value=25 Score=33.92 Aligned_cols=37 Identities=22% Similarity=0.556 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 290 ENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 290 ~~~~~i~~~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
+...|... -|.||+|+.+.+-..|=-.+.|. .|++.+
T Consensus 103 ~l~~w~~~-~RFCg~CG~~~~~~~~g~~~~C~-~cg~~~ 139 (279)
T COG2816 103 QLLEWYRS-HRFCGRCGTKTYPREGGWARVCP-KCGHEH 139 (279)
T ss_pred HHHHHHhh-CcCCCCCCCcCccccCceeeeCC-CCCCcc
Confidence 34456443 48999999999988777778888 788765
No 221
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=41.75 E-value=17 Score=19.62 Aligned_cols=16 Identities=44% Similarity=0.978 Sum_probs=13.1
Q ss_pred cccccCCcCCCCCCch
Q 014105 261 FCWNCTEEAHRPVDCD 276 (430)
Q Consensus 261 fC~~C~~~~H~~~~C~ 276 (430)
.|++|++.-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5999999999877664
No 222
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.74 E-value=23 Score=24.03 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=4.8
Q ss_pred CCCCCCCcce
Q 014105 300 KPCPRCKRPI 309 (430)
Q Consensus 300 k~CP~C~~~I 309 (430)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 3455554444
No 223
>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=41.61 E-value=21 Score=20.98 Aligned_cols=7 Identities=57% Similarity=1.621 Sum_probs=3.8
Q ss_pred CCCCCCC
Q 014105 300 KPCPRCK 306 (430)
Q Consensus 300 k~CP~C~ 306 (430)
-.||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 3566654
No 224
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=41.58 E-value=19 Score=29.19 Aligned_cols=17 Identities=29% Similarity=0.798 Sum_probs=16.0
Q ss_pred cCCCcccHHHHHHHHHh
Q 014105 160 ACGHPFCSSCWTGYIST 176 (430)
Q Consensus 160 ~CgH~fC~~Cl~~yi~~ 176 (430)
.|+|.|-.-|+.+++.+
T Consensus 80 ~CNHaFH~hCisrWlkt 96 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT 96 (114)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 49999999999999998
No 225
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=41.49 E-value=20 Score=27.60 Aligned_cols=17 Identities=29% Similarity=0.804 Sum_probs=16.1
Q ss_pred cCCCcccHHHHHHHHHh
Q 014105 160 ACGHPFCSSCWTGYIST 176 (430)
Q Consensus 160 ~CgH~fC~~Cl~~yi~~ 176 (430)
.|.|.|-..|+.+++.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 49999999999999998
No 226
>PF15616 TerY-C: TerY-C metal binding domain
Probab=41.20 E-value=16 Score=31.08 Aligned_cols=24 Identities=29% Similarity=0.809 Sum_probs=16.7
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCcccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCW 330 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw 330 (430)
.--||.|+... ....|. ||..|||
T Consensus 77 ~PgCP~CGn~~------~fa~C~--CGkl~Ci 100 (131)
T PF15616_consen 77 APGCPHCGNQY------AFAVCG--CGKLFCI 100 (131)
T ss_pred CCCCCCCcChh------cEEEec--CCCEEEe
Confidence 36899999885 235564 7777775
No 227
>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=41.08 E-value=11 Score=26.37 Aligned_cols=26 Identities=23% Similarity=0.681 Sum_probs=15.7
Q ss_pred CCCCCCCcceeecCCC--CceEecCCCcc
Q 014105 300 KPCPRCKRPIEKNQGC--MHMTCTPPCKF 326 (430)
Q Consensus 300 k~CP~C~~~IeK~~GC--nhm~C~~~C~~ 326 (430)
-+|++|++.+-+.++= -.|.|. +|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCp-RC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCP-RCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECC-CCCc
Confidence 4677777777664332 356776 5654
No 228
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=40.94 E-value=60 Score=36.58 Aligned_cols=34 Identities=24% Similarity=0.183 Sum_probs=18.3
Q ss_pred EecHHHHHHHHHHHHHHHHhHcCCCHHHHHHHHHhcC
Q 014105 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYN 105 (430)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (430)
.|.+-|..+.+.+-+..+++ -.+.....|+++..
T Consensus 954 ~LD~VD~f~~f~~~i~~lq~---~d~~~yq~l~~~L~ 987 (1010)
T KOG1991|consen 954 PLDQVDPFQLFKEAITNLQS---SDAVRYQKLISTLT 987 (1010)
T ss_pred cccccchHHHHHHHHHhhhc---cChHHHHHHHhcCC
Confidence 45666666666666555543 23444445554443
No 229
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=40.15 E-value=17 Score=25.96 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=16.8
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCcc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
+.-.||.|+.+.. .|-.|. .||+
T Consensus 25 ~l~~C~~cG~~~~-----~H~vc~-~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKL-----PHRVCP-SCGY 47 (55)
T ss_pred cceECCCCCCccc-----CeeECC-ccCe
Confidence 3467999999887 677776 5664
No 230
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=40.12 E-value=7.7 Score=37.55 Aligned_cols=53 Identities=25% Similarity=0.773 Sum_probs=37.5
Q ss_pred CCCceecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCC
Q 014105 227 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRC 305 (430)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C 305 (430)
++.+-+|-. |+..|.+- + .= .|.+.||+.|... |. .|.||.|
T Consensus 87 ~p~VHfCd~--Cd~PI~IY-G------RmIPCkHvFCl~CAr~-~~---------------------------dK~Cp~C 129 (389)
T KOG2932|consen 87 GPRVHFCDR--CDFPIAIY-G------RMIPCKHVFCLECARS-DS---------------------------DKICPLC 129 (389)
T ss_pred CcceEeecc--cCCcceee-e------cccccchhhhhhhhhc-Cc---------------------------cccCcCc
Confidence 456677874 88776543 1 22 5899999999632 32 1899999
Q ss_pred CcceeecCCCC
Q 014105 306 KRPIEKNQGCM 316 (430)
Q Consensus 306 ~~~IeK~~GCn 316 (430)
.-.|+|.+-|.
T Consensus 130 ~d~VqrIeq~~ 140 (389)
T KOG2932|consen 130 DDRVQRIEQIM 140 (389)
T ss_pred ccHHHHHHHhc
Confidence 99999887774
No 231
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=40.06 E-value=7 Score=42.15 Aligned_cols=51 Identities=20% Similarity=0.490 Sum_probs=38.9
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhh
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~ 201 (430)
..+|+||+..+ ..++.+.|.|.||..||..-+...-. ...|| .|+..+...
T Consensus 21 ~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~~------~~~~~--lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKKG------PKQCA--LCKSDIEKR 71 (684)
T ss_pred hccCCceeEEe--eccchhhhhHHHHhhhhhceeeccCc------cccch--hhhhhhhhh
Confidence 56799999887 45578899999999999988776432 46788 787665443
No 232
>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=39.30 E-value=20 Score=26.51 Aligned_cols=17 Identities=24% Similarity=0.727 Sum_probs=12.2
Q ss_pred cccHHHHHHHHHhhhcC
Q 014105 164 PFCSSCWTGYISTAIND 180 (430)
Q Consensus 164 ~fC~~Cl~~yi~~~i~~ 180 (430)
-||+.||..|+..+-..
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999877654
No 233
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=39.10 E-value=20 Score=24.06 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=15.2
Q ss_pred cCCCCCCceEEeecCCCCceEEe-cCCCccccccCC
Q 014105 233 CPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTE 267 (430)
Q Consensus 233 CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~ 267 (430)
|..++|.... ...+.| .|+..||..++.
T Consensus 1 C~~~~C~~~~-------~~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 1 CSFPGCKKKD-------FLPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp -SSTTT--BC-------TSHEE-TTTS-EE-TTTHS
T ss_pred CccCcCcCcc-------CCCeECCCCCcccCccccC
Confidence 4455676532 246899 799999999874
No 234
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=38.93 E-value=33 Score=21.44 Aligned_cols=25 Identities=20% Similarity=0.608 Sum_probs=21.8
Q ss_pred CCCCCCcceeecCCCCceEecCCCcc
Q 014105 301 PCPRCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
.|+.|+.++.-..|=..+.|. .|++
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs-~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCA-LCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECC-CCCe
Confidence 699999999999999999998 6764
No 235
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.85 E-value=16 Score=41.15 Aligned_cols=32 Identities=22% Similarity=0.507 Sum_probs=25.3
Q ss_pred hcCCCCCCCCcceeecCCCCceEecCCCcc-----ccccccccc
Q 014105 297 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKF-----EFCWLCLGQ 335 (430)
Q Consensus 297 ~~tk~CP~C~~~IeK~~GCnhm~C~~~C~~-----~FCw~C~~~ 335 (430)
...+.||.|+... ....|. .||. .||-.|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP-~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCP-FCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCC-CCCCCCCcceeCccccCc
Confidence 3468999999885 558898 8996 499999754
No 236
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=38.79 E-value=42 Score=24.76 Aligned_cols=32 Identities=31% Similarity=0.529 Sum_probs=19.1
Q ss_pred CceecCCCCCCceEEeecCCCCceEEe-cCCCcc
Q 014105 229 KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (430)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (430)
.++.||.-+|..+.... ..+-..+.| .|+...
T Consensus 5 ~lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA-ISGYYRAKCNGCESRT 37 (64)
T ss_pred cccCCCCCCCceeEEEe-cCceEEEEcCCCCcCc
Confidence 56789975554433332 234456788 788753
No 237
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=38.14 E-value=14 Score=28.98 Aligned_cols=35 Identities=29% Similarity=0.737 Sum_probs=27.4
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccccccccccccccC
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (430)
--||.|+.| ...|--+.+. |++.|=..|...|-.-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~--C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK--CSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeecc--CccHHHHHHHHHHHcc
Confidence 458888887 3567767775 9999999999999653
No 238
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=37.75 E-value=16 Score=40.89 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHhHc-CCCHHHHHH
Q 014105 75 IRQRQEEDITRISTVL-SISKVAASI 99 (430)
Q Consensus 75 i~~~~~~~i~~v~~~l-~i~~~~a~~ 99 (430)
|...|..+-.+...++ .+++.....
T Consensus 968 i~~lq~~d~~~yq~l~~~L~~~q~~~ 993 (1010)
T KOG1991|consen 968 ITNLQSSDAVRYQKLISTLTPEQQDS 993 (1010)
T ss_pred HHhhhccChHHHHHHHhcCCHHHHHH
Confidence 3344444444444333 345554433
No 239
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.24 E-value=30 Score=32.62 Aligned_cols=20 Identities=25% Similarity=0.306 Sum_probs=15.0
Q ss_pred CCHHHHHHHHHhcCCChhhh
Q 014105 92 ISKVAASILLRFYNWSVSKV 111 (430)
Q Consensus 92 i~~~~a~~LL~~~~W~~~~l 111 (430)
|+...|.+|++.|.=|-..+
T Consensus 8 vs~~~a~~lmRrf~~~h~~v 27 (278)
T PF15135_consen 8 VSSEKAGALMRRFGSNHTGV 27 (278)
T ss_pred cchHHHHHHHHhccccccch
Confidence 56778899999998665444
No 240
>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=36.99 E-value=18 Score=25.87 Aligned_cols=22 Identities=36% Similarity=0.857 Sum_probs=16.2
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 325 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~ 325 (430)
+...||.|+.+.. .|..|. .||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~-~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCP-SCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCT-TTB
T ss_pred ceeeeccCCCEec-----ccEeeC-CCC
Confidence 4568999998876 667776 565
No 241
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.97 E-value=27 Score=33.02 Aligned_cols=55 Identities=27% Similarity=0.568 Sum_probs=37.7
Q ss_pred CccccccccccccCCCe--eeccCC-----CcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 140 EEMTCGICFENYPSDRL--LAAACG-----HPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~Cg-----H~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
.+..|=|||.+-..+.. ..-||. |-....|+..||..+-. |.....+.|| +|...
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~-~n~~q~V~C~--QCqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQR-GNPLQTVSCP--QCQTE 80 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhc-CCCCceeech--hhcch
Confidence 35679999986432221 123554 45889999999988766 3334589999 89875
No 242
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=36.82 E-value=31 Score=24.22 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=22.8
Q ss_pred ccccccccccCCCeeeccCCCcccHHHHHHH
Q 014105 143 TCGICFENYPSDRLLAAACGHPFCSSCWTGY 173 (430)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y 173 (430)
.|.||......-..+.+.=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999988755444556677 8999999876
No 243
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=36.61 E-value=36 Score=32.52 Aligned_cols=35 Identities=17% Similarity=0.542 Sum_probs=25.5
Q ss_pred HHHHHhcCCCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 292 MNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 292 ~~~i~~~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
..|- .+.+-||.|+.++....|=..+.|. .|+...
T Consensus 93 ~~w~-~~~~fC~~CG~~~~~~~~~~~~~C~-~c~~~~ 127 (256)
T PRK00241 93 AEFY-RSHRFCGYCGHPMHPSKTEWAMLCP-HCRERY 127 (256)
T ss_pred HHHh-hcCccccccCCCCeecCCceeEECC-CCCCEE
Confidence 3452 3469999999998876555678998 788543
No 244
>PRK12495 hypothetical protein; Provisional
Probab=35.96 E-value=49 Score=30.70 Aligned_cols=17 Identities=29% Similarity=0.733 Sum_probs=13.4
Q ss_pred CCCCCCCCcceeecCCC
Q 014105 299 SKPCPRCKRPIEKNQGC 315 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GC 315 (430)
.+.||.|+.+|-+..|+
T Consensus 42 a~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ 58 (226)
T ss_pred hhhcccccCcccCCCCe
Confidence 57999999999855444
No 245
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=35.74 E-value=29 Score=37.60 Aligned_cols=20 Identities=20% Similarity=0.220 Sum_probs=12.2
Q ss_pred hhhhhHHH--------HHhhhHHHHHHH
Q 014105 376 ERYTHYYE--------RWATNQSSRQKA 395 (430)
Q Consensus 376 ~ry~~y~~--------r~~~~~~s~~~~ 395 (430)
..|.+||. +.+++..+.|.+
T Consensus 666 K~yNpfYa~lA~KfCe~~~~~~~tfQF~ 693 (822)
T KOG2141|consen 666 KTYNPFYALLALKFCEFNKNLKKTFQFA 693 (822)
T ss_pred cccchHHHHHHHHHHHHhhhhHHHHHHH
Confidence 67888885 344555555644
No 246
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=35.67 E-value=19 Score=27.91 Aligned_cols=29 Identities=31% Similarity=0.723 Sum_probs=14.6
Q ss_pred CCCCCCCCc------ceeecCCCCceEecCCCcccc
Q 014105 299 SKPCPRCKR------PIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 299 tk~CP~C~~------~IeK~~GCnhm~C~~~C~~~F 328 (430)
+-.||.|+. .|.|..|=-+++|+ .||..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~-~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCR-VCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEES-SS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEec-CCCCeE
Confidence 358999982 23355677788888 676554
No 247
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=35.66 E-value=19 Score=40.33 Aligned_cols=26 Identities=38% Similarity=1.026 Sum_probs=21.1
Q ss_pred CCCCCCCc-ceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~-~IeK~~GCnhm~C~~~C~~~F 328 (430)
-.||-|+. .|+..|||| +|+ .|+.+.
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~-~c~~~~ 854 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCT-NCGAQL 854 (858)
T ss_pred CCCCccCCCceeecCCCc--ccc-chhhhh
Confidence 48999975 678999998 698 788753
No 248
>PHA02664 hypothetical protein; Provisional
Probab=35.44 E-value=66 Score=31.49 Aligned_cols=13 Identities=31% Similarity=0.261 Sum_probs=4.9
Q ss_pred HHHHHHHHHHhHc
Q 014105 78 RQEEDITRISTVL 90 (430)
Q Consensus 78 ~~~~~i~~v~~~l 90 (430)
.++++..+-..+|
T Consensus 513 ~ieee~~ee~~vl 525 (534)
T PHA02664 513 AIEEEEEEERAVL 525 (534)
T ss_pred hhhHHHHHHHHHH
Confidence 3333333333333
No 249
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=35.41 E-value=18 Score=36.74 Aligned_cols=11 Identities=18% Similarity=0.513 Sum_probs=6.8
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
-+|--|+..+.
T Consensus 428 Y~CEDCg~~LS 438 (468)
T KOG1701|consen 428 YKCEDCGLLLS 438 (468)
T ss_pred eehhhcCcccc
Confidence 45666666665
No 250
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=35.41 E-value=39 Score=27.99 Aligned_cols=29 Identities=21% Similarity=0.659 Sum_probs=19.8
Q ss_pred ceecCCCCCCceEEeecCCCCceEEe-cCCCc
Q 014105 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (430)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (430)
+++||. |+..+............| .||+.
T Consensus 2 m~FCp~--Cgsll~p~~~~~~~~l~C~kCgye 31 (113)
T COG1594 2 MRFCPK--CGSLLYPKKDDEGGKLVCRKCGYE 31 (113)
T ss_pred ccccCC--ccCeeEEeEcCCCcEEECCCCCcc
Confidence 468995 999887754333446777 67765
No 251
>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=35.39 E-value=22 Score=22.39 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=4.6
Q ss_pred CCCCCCCcce
Q 014105 300 KPCPRCKRPI 309 (430)
Q Consensus 300 k~CP~C~~~I 309 (430)
-+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 3555555444
No 252
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=35.37 E-value=27 Score=31.63 Aligned_cols=27 Identities=30% Similarity=0.705 Sum_probs=21.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-.||+|+.++.+ .+.|+|.|. .|++..
T Consensus 150 a~~~~~g~~~~~-~~~~~~~c~-~~~~~e 176 (189)
T PRK09521 150 AMCSRCRTPLVK-KGENELKCP-NCGNIE 176 (189)
T ss_pred EEccccCCceEE-CCCCEEECC-CCCCEE
Confidence 379999999987 455999998 787643
No 253
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=35.29 E-value=26 Score=39.97 Aligned_cols=60 Identities=23% Similarity=0.619 Sum_probs=40.4
Q ss_pred ecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCccee
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~Ie 310 (430)
-|-. |+--|... ..+..-|-| .|++-.|..|- ++.+ +..++-||+|++...
T Consensus 19 iCqI--CGD~vg~~-~~Ge~FVAC~eC~FPVCrpCY----------EYEr---------------~eG~q~CPqCktrYk 70 (1079)
T PLN02638 19 VCQI--CGDNVGKT-VDGEPFVACDVCAFPVCRPCY----------EYER---------------KDGNQSCPQCKTKYK 70 (1079)
T ss_pred eeee--cccccCcC-CCCCEEEEeccCCCccccchh----------hhhh---------------hcCCccCCccCCchh
Confidence 4553 77665554 345677999 89999998775 1111 122388999999988
Q ss_pred ecCCCCceE
Q 014105 311 KNQGCMHMT 319 (430)
Q Consensus 311 K~~GCnhm~ 319 (430)
+--||..+-
T Consensus 71 r~kgsprv~ 79 (1079)
T PLN02638 71 RHKGSPAIL 79 (1079)
T ss_pred hhcCCCCcC
Confidence 777777654
No 254
>PLN02189 cellulose synthase
Probab=35.09 E-value=30 Score=39.38 Aligned_cols=61 Identities=23% Similarity=0.652 Sum_probs=41.3
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCcce
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~I 309 (430)
.-|.. |+--|... ..+..-|-| .|++-.|..|- + +. .+..++.||+|++..
T Consensus 35 ~~C~i--Cgd~vg~~-~~g~~fvaC~~C~fpvCr~Cy-e---------ye---------------r~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 35 QVCEI--CGDEIGLT-VDGDLFVACNECGFPVCRPCY-E---------YE---------------RREGTQNCPQCKTRY 86 (1040)
T ss_pred ccccc--cccccCcC-CCCCEEEeeccCCCccccchh-h---------hh---------------hhcCCccCcccCCch
Confidence 35664 77666554 345677999 89999998885 1 11 012238899999999
Q ss_pred eecCCCCceE
Q 014105 310 EKNQGCMHMT 319 (430)
Q Consensus 310 eK~~GCnhm~ 319 (430)
.+--|++.+.
T Consensus 87 ~r~kgs~~v~ 96 (1040)
T PLN02189 87 KRLKGSPRVE 96 (1040)
T ss_pred hhccCCCCcC
Confidence 8777777654
No 255
>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=35.08 E-value=23 Score=23.02 Aligned_cols=12 Identities=25% Similarity=0.946 Sum_probs=6.3
Q ss_pred CCCCCCCcceee
Q 014105 300 KPCPRCKRPIEK 311 (430)
Q Consensus 300 k~CP~C~~~IeK 311 (430)
..||.|+..++|
T Consensus 27 ~~CP~Cg~~~~r 38 (41)
T smart00834 27 ATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCccee
Confidence 456666555443
No 256
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=35.01 E-value=36 Score=32.32 Aligned_cols=48 Identities=17% Similarity=0.393 Sum_probs=35.1
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCC
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (430)
...|||=+-.+ ...+++-.|||.|=++=+..++... ..++||..+|..
T Consensus 176 s~rdPis~~~I-~nPviSkkC~HvydrDsI~~~l~~~-------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPI-VNPVISKKCGHVYDRDSIMQILCDE-------ITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhh-hchhhhcCcCcchhhhhHHHHhccC-------ceeecccccCCc
Confidence 45688855443 2455677899999998888777652 268999999993
No 257
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.70 E-value=35 Score=30.38 Aligned_cols=8 Identities=50% Similarity=0.692 Sum_probs=3.6
Q ss_pred CCCCCccc
Q 014105 51 DSDDSDDL 58 (430)
Q Consensus 51 ~~d~~d~~ 58 (430)
+++|+++.
T Consensus 213 ~~edsde~ 220 (227)
T KOG3241|consen 213 DLEDSDEN 220 (227)
T ss_pred cccccccc
Confidence 33455443
No 258
>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=34.66 E-value=62 Score=21.92 Aligned_cols=28 Identities=18% Similarity=0.477 Sum_probs=17.5
Q ss_pred cCCCCCCCCcc-eeecCCCCceEecCCCcc
Q 014105 298 NSKPCPRCKRP-IEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 298 ~tk~CP~C~~~-IeK~~GCnhm~C~~~C~~ 326 (430)
+.-.||+|+.. +-+..+=....|. .|++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~-~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCK-ACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECC-CCCC
Confidence 44569999974 3334444556676 6765
No 259
>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=34.61 E-value=47 Score=27.59 Aligned_cols=36 Identities=25% Similarity=0.534 Sum_probs=27.2
Q ss_pred cCCCCCCCCcceeecCCCCceEecCCCccccccccccc
Q 014105 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (430)
Q Consensus 298 ~tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (430)
+.+.|..|+.+.-...+.. ..|. .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~-~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCV-DCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEET-TTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCC-cCCccccCccCCc
Confidence 4678999998876555555 8898 8999999999865
No 260
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=34.58 E-value=43 Score=19.89 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=20.0
Q ss_pred CCCCCcceeecCCCCceEecCCCcc
Q 014105 302 CPRCKRPIEKNQGCMHMTCTPPCKF 326 (430)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (430)
|-+|++++.-..|=.++.|. .|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa-~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCA-CCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECC-ccCc
Confidence 66888888888899999998 6764
No 261
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=34.17 E-value=42 Score=29.48 Aligned_cols=49 Identities=20% Similarity=0.473 Sum_probs=34.1
Q ss_pred CCccccccccccccCCCeeeccCC--C---cccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 139 GEEMTCGICFENYPSDRLLAAACG--H---PFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~Cg--H---~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
.....|-||++... . ..-||. . ....+|+..|+..+ + ..+|| .|+..+.
T Consensus 6 ~~~~~CRIC~~~~~-~--~~~PC~CkGs~k~VH~sCL~rWi~~s---~----~~~Ce--iC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEYD-V--VTNYCNCKNENKIVHKECLEEWINTS---K----NKSCK--ICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCCC-C--ccCCcccCCCchHHHHHHHHHHHhcC---C----CCccc--ccCCeEE
Confidence 34567999998753 2 223554 3 46899999999963 2 46899 8988753
No 262
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.77 E-value=17 Score=34.78 Aligned_cols=31 Identities=23% Similarity=0.788 Sum_probs=21.6
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (430)
++.||-|+.+=- +.++=. +|+|-+||.|...
T Consensus 239 ~~~C~~Cg~~Pt-----iP~~~~-~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPT-----IPHVIG-KCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCC-----CCeeec-cccceeehhhhhh
Confidence 578999986543 333333 4888888999764
No 263
>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=33.25 E-value=24 Score=32.98 Aligned_cols=54 Identities=20% Similarity=0.321 Sum_probs=33.4
Q ss_pred cccCCCCCCCCc-hhhHHHhhcChHHHHHHHHHHHHHHHhcCCCceecCCCCCCceEEe
Q 014105 187 LRCPDPSCGAAV-GQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (430)
Q Consensus 187 i~CP~~~C~~~l-~~~~i~~ll~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~ 244 (430)
-+|| .|+.-. ....|.-|++++-+.+.-.--....... ....||.|+|+.++..
T Consensus 11 ~~CP--vCksDrYLnPdik~linPECyHrmCESCvdRIFs~--GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCP--VCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR--GPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCC--ccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC--CCCCCCCccHHHHHHH
Confidence 3799 788742 2334566778877766544333332322 3368999999987643
No 264
>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=32.97 E-value=21 Score=25.11 Aligned_cols=45 Identities=18% Similarity=0.436 Sum_probs=24.1
Q ss_pred ccccccccccccCCCeeeccCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchhhHH
Q 014105 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~~~i 203 (430)
.+.||.|...+... =|..++...=.... ..+.|| .|...+...++
T Consensus 2 ~f~CP~C~~~~~~~--------------~L~~H~~~~H~~~~--~~v~CP--iC~~~~~~~l~ 46 (54)
T PF05605_consen 2 SFTCPYCGKGFSES--------------SLVEHCEDEHRSES--KNVVCP--ICSSRVTDNLI 46 (54)
T ss_pred CcCCCCCCCccCHH--------------HHHHHHHhHCcCCC--CCccCC--CchhhhhhHHH
Confidence 57899998744211 12334433322221 268999 88865444333
No 265
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=32.70 E-value=46 Score=21.83 Aligned_cols=21 Identities=29% Similarity=1.024 Sum_probs=12.9
Q ss_pred CCCCCCCccee-ec--CCCCceEec
Q 014105 300 KPCPRCKRPIE-KN--QGCMHMTCT 321 (430)
Q Consensus 300 k~CP~C~~~Ie-K~--~GCnhm~C~ 321 (430)
+.||.|+..+. |. .| ..+.|+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECC
Confidence 57999986554 22 34 556665
No 266
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=32.53 E-value=30 Score=31.27 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=19.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
-.|++|+.++++ .=+.|+|. .||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp-~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCP-NCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECC-CCCCE
Confidence 479999999998 44678897 78764
No 267
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=32.18 E-value=44 Score=30.74 Aligned_cols=19 Identities=21% Similarity=0.595 Sum_probs=14.9
Q ss_pred CCceecCCCCCCceEEeec
Q 014105 228 RKTKWCPAPGCDYAVDFVV 246 (430)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~ 246 (430)
....-||+|+|..+|...+
T Consensus 136 SqRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDP 154 (275)
T ss_pred cceeccCCCCcceeeecCC
Confidence 3457899999999987643
No 268
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.14 E-value=17 Score=37.73 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=19.6
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (430)
--.||-|-.+-. .-+...|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 368999976544 222225888888888754
No 269
>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=32.07 E-value=37 Score=35.87 Aligned_cols=35 Identities=20% Similarity=0.579 Sum_probs=23.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc-----cccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (430)
-.||+|..++.--..=|.+.|. .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCH-YCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcC-CCcCcCCCCCCCCCCCCC
Confidence 4678887776533333478887 78876 58888763
No 270
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=31.78 E-value=33 Score=37.36 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=29.7
Q ss_pred CccccccccccccCCCeeeccCCCcccHHHHHHHHHh
Q 014105 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (430)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~ 176 (430)
..+.|.||.-.+.....+...|+|.-..+|...||+.
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc
Confidence 3567888876555556667789999999999999987
No 271
>smart00336 BBOX B-Box-type zinc finger.
Probab=31.60 E-value=52 Score=21.22 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=25.4
Q ss_pred CCCCCCC-cceeecCCCCceEecCCCccccccccccccccCC
Q 014105 300 KPCPRCK-RPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (430)
Q Consensus 300 k~CP~C~-~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (430)
..|+.|. .++. ++|. .|....|..|... .|.
T Consensus 4 ~~C~~h~~~~~~-------~~C~-~c~~~iC~~C~~~--~H~ 35 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCE-ECGALLCRTCDEA--EHR 35 (42)
T ss_pred CcCCCCCCCceE-------EECC-CCCcccccccChh--hcC
Confidence 5799997 7777 9998 8999999999854 454
No 272
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=31.34 E-value=37 Score=27.69 Aligned_cols=26 Identities=31% Similarity=1.041 Sum_probs=17.6
Q ss_pred CCCCCCCccee-ecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (430)
.+||+|..-.- ..++ +|.|. .|.++|
T Consensus 4 p~cp~c~sEytYed~~--~~~cp-ec~~ew 30 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICP-ECAHEW 30 (112)
T ss_pred CCCCccCCceEEecCc--eEeCc-hhcccc
Confidence 68999976544 4555 78887 566543
No 273
>PLN02436 cellulose synthase A
Probab=31.32 E-value=41 Score=38.38 Aligned_cols=50 Identities=28% Similarity=0.734 Sum_probs=34.4
Q ss_pred CCccccccccccccC----CCeeecc-CCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPS----DRLLAAA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~----~~~~~l~-CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.....|.||.+++.. +.++... |+-..|+.|. +|-.. +| .-.|| .|+...
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~---eg----~~~Cp--qckt~Y 88 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERR---EG----NQACP--QCKTRY 88 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---cC----CccCc--ccCCch
Confidence 345589999998643 2344454 8889999999 55443 45 34799 788764
No 274
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.84 E-value=55 Score=23.39 Aligned_cols=29 Identities=31% Similarity=0.605 Sum_probs=14.9
Q ss_pred CceecCCCCCCceEEeecCCCC------ceEEe-cCCC
Q 014105 229 KTKWCPAPGCDYAVDFVVGSGN------YDVTC-RCSY 259 (430)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~------~~v~C-~C~~ 259 (430)
.++.||. |+........... ..|.| .||.
T Consensus 2 ~LkPCPF--CG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPF--CGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCC--CCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678986 7644333211111 45667 5655
No 275
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=30.57 E-value=77 Score=22.40 Aligned_cols=37 Identities=22% Similarity=0.106 Sum_probs=31.0
Q ss_pred EecHHHHHHHHHHHHHHHHhHcCCCHHHHHHHHHhcC
Q 014105 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYN 105 (430)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (430)
-||-++|.+.+.--+.+++..|+|+...-.-+-+.++
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3688899999999999999999999888777777654
No 276
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.29 E-value=62 Score=26.20 Aligned_cols=56 Identities=16% Similarity=0.232 Sum_probs=31.1
Q ss_pred cCCCceecCCCCCCce-EEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhh
Q 014105 226 DNRKTKWCPAPGCDYA-VDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNS 286 (430)
Q Consensus 226 ~~~~~~~CP~p~C~~~-i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~ 286 (430)
..+.+..||+ |+.. +......+...+.| .||+.+=.. ..+....=+.+..|+....
T Consensus 17 klpt~f~CP~--Cge~~v~v~~~k~~~h~~C~~CG~y~~~~---V~~l~epIDVY~~wiD~~~ 74 (99)
T PRK14892 17 KLPKIFECPR--CGKVSISVKIKKNIAIITCGNCGLYTEFE---VPSVYDEVDVYNKFIDLYL 74 (99)
T ss_pred CCCcEeECCC--CCCeEeeeecCCCcceEECCCCCCccCEE---CCccccchhhHHHHHHHHH
Confidence 3457789996 8843 32222234456778 787764221 2232233467788876553
No 277
>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=30.10 E-value=31 Score=24.19 Aligned_cols=34 Identities=24% Similarity=0.579 Sum_probs=24.1
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccccccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~ 336 (430)
+.|+.|++..-. .=..-.|+ .||..||..|....
T Consensus 3 ~~C~~C~~~F~~--~~rk~~Cr-~Cg~~~C~~C~~~~ 36 (57)
T cd00065 3 SSCMGCGKPFTL--TRRRHHCR-NCGRIFCSKCSSNR 36 (57)
T ss_pred CcCcccCccccC--CccccccC-cCcCCcChHHcCCe
Confidence 678888766543 22346688 79999999998643
No 278
>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=30.03 E-value=53 Score=23.39 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=19.2
Q ss_pred ecCCCCCCceEEeecCCCCceEEe-cCCCcc
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (430)
-|| .|+..|.+........+.| .||..+
T Consensus 4 ~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 577 4998887754333457788 788765
No 279
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.01 E-value=25 Score=25.83 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=11.3
Q ss_pred CCCCCCCCcceee
Q 014105 299 SKPCPRCKRPIEK 311 (430)
Q Consensus 299 tk~CP~C~~~IeK 311 (430)
+.+||.|+++++.
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5899999999974
No 280
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=29.84 E-value=69 Score=23.82 Aligned_cols=30 Identities=23% Similarity=0.462 Sum_probs=20.8
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCcccc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (430)
+.|| +|++.-..- +.....|.| .||...+.
T Consensus 20 VkCp--dC~N~q~vF-shast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP--DCGNEQVVF-SHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECC--CCCCEEEEe-ccCceEEEecccccEEEe
Confidence 6788 698754433 345678999 89988763
No 281
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.76 E-value=55 Score=29.22 Aligned_cols=59 Identities=24% Similarity=0.612 Sum_probs=36.4
Q ss_pred Ccccccccccccc-CC---C-eeeccCCCcccHHHHHHHHHhhhcCCCc--eeecccCCCCCCCCchh
Q 014105 140 EEMTCGICFENYP-SD---R-LLAAACGHPFCSSCWTGYISTAINDGPG--CLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 140 ~~~~C~IC~e~~~-~~---~-~~~l~CgH~fC~~Cl~~yi~~~i~~g~~--~~~i~CP~~~C~~~l~~ 200 (430)
....|+||+-.-- .. . .-...||..|..-|+..|++.-+....+ +..=.|| -|..++..
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pial 229 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIAL 229 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCccee
Confidence 3456777775311 11 1 1134699999999999999876655432 2233688 78877643
No 282
>COG4640 Predicted membrane protein [Function unknown]
Probab=29.65 E-value=27 Score=35.09 Aligned_cols=23 Identities=39% Similarity=0.964 Sum_probs=13.1
Q ss_pred CCCCCCC-cceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCK-RPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~-~~IeK~~GCnhm~C~~~C~~~F 328 (430)
+.||+|| .-.| .-|.|+ +||+.|
T Consensus 2 ~fC~kcG~qk~E-----d~~qC~-qCG~~~ 25 (465)
T COG4640 2 KFCPKCGSQKAE-----DDVQCT-QCGHKF 25 (465)
T ss_pred Cccccccccccc-----cccccc-ccCCcC
Confidence 6788888 4443 234466 565543
No 283
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=29.62 E-value=55 Score=27.78 Aligned_cols=22 Identities=41% Similarity=1.115 Sum_probs=11.5
Q ss_pred CCCCC--CCcceeecCCCCceEecCCCccc
Q 014105 300 KPCPR--CKRPIEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~--C~~~IeK~~GCnhm~C~~~C~~~ 327 (430)
|+||+ |.-.++ ++-|+..||+.
T Consensus 83 k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 83 KPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp SB-SS--S--BEE------EE---TBTTB-
T ss_pred CCCCccccCCcee------EEeccCcCCCc
Confidence 99999 998887 68887456654
No 284
>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=29.42 E-value=93 Score=33.85 Aligned_cols=6 Identities=0% Similarity=-0.108 Sum_probs=2.6
Q ss_pred CCCCCc
Q 014105 193 SCGAAV 198 (430)
Q Consensus 193 ~C~~~l 198 (430)
.|+..+
T Consensus 352 ~~~Q~y 357 (622)
T PF02724_consen 352 QAQQKY 357 (622)
T ss_pred HHcCCc
Confidence 444443
No 285
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.39 E-value=40 Score=30.56 Aligned_cols=17 Identities=41% Similarity=1.040 Sum_probs=7.2
Q ss_pred CccccccCCcCCCCCCc
Q 014105 259 YSFCWNCTEEAHRPVDC 275 (430)
Q Consensus 259 ~~fC~~C~~~~H~~~~C 275 (430)
+..|+.|...-|.-..|
T Consensus 78 ~~iC~~C~~~~H~s~~C 94 (190)
T COG5082 78 HSICYNCSWDGHRSNHC 94 (190)
T ss_pred hhHhhhcCCCCcccccC
Confidence 34444443344444433
No 286
>PHA02325 hypothetical protein
Probab=29.00 E-value=26 Score=25.71 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=8.9
Q ss_pred cCCCCCCCCcce
Q 014105 298 NSKPCPRCKRPI 309 (430)
Q Consensus 298 ~tk~CP~C~~~I 309 (430)
++|.||+|+..-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 468899988654
No 287
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=28.84 E-value=40 Score=30.00 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHH
Q 014105 72 EADIRQRQEEDIT 84 (430)
Q Consensus 72 ~~~i~~~~~~~i~ 84 (430)
.+++.+.+.+.+.
T Consensus 62 e~dFeref~kmm~ 74 (170)
T PF04050_consen 62 EEDFEREFQKMMA 74 (170)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3466665555544
No 288
>PLN02400 cellulose synthase
Probab=28.06 E-value=54 Score=37.60 Aligned_cols=60 Identities=27% Similarity=0.708 Sum_probs=39.9
Q ss_pred ecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCccee
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~Ie 310 (430)
-|-. |+--|-.. ..+..-|-| .|+.-.|.-|- ++-+ +..++-||+|++...
T Consensus 38 iCqI--CGD~VG~t-~dGe~FVAC~eCaFPVCRpCY-EYER------------------------keGnq~CPQCkTrYk 89 (1085)
T PLN02400 38 ICQI--CGDDVGVT-ETGDVFVACNECAFPVCRPCY-EYER------------------------KDGTQCCPQCKTRYR 89 (1085)
T ss_pred eeee--cccccCcC-CCCCEEEEEccCCCccccchh-heec------------------------ccCCccCcccCCccc
Confidence 4543 66555444 345677999 89999998886 2110 112378999999988
Q ss_pred ecCCCCceE
Q 014105 311 KNQGCMHMT 319 (430)
Q Consensus 311 K~~GCnhm~ 319 (430)
+-.|+..+.
T Consensus 90 R~KgsprV~ 98 (1085)
T PLN02400 90 RHKGSPRVE 98 (1085)
T ss_pred cccCCCCCC
Confidence 777777653
No 289
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=27.18 E-value=57 Score=23.67 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.0
Q ss_pred CCCCCCCcc----eeecCCCCceEecCCCccc
Q 014105 300 KPCPRCKRP----IEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~----IeK~~GCnhm~C~~~C~~~ 327 (430)
-.||+|+.+ +-+..|=.++.|. .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv-~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECV-ECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-cCCCc
Confidence 479999864 3355666889998 78875
No 290
>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=26.67 E-value=75 Score=25.94 Aligned_cols=34 Identities=18% Similarity=0.479 Sum_probs=22.2
Q ss_pred CCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCC
Q 014105 162 GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (430)
Q Consensus 162 gH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (430)
.-.||..||..-+...+.+-.....-.|| .|..+
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECC--CCCCe
Confidence 66799999998877655432111256798 66653
No 291
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=26.58 E-value=41 Score=26.66 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=23.1
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
-.||.|+..-.|..+----.|. .|+..|
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~-~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCK-KCGKKF 63 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEET-TTTEEE
T ss_pred CcCCCCCCceeEEeeeEEeecC-CCCCEE
Confidence 5899999998888777778888 787765
No 292
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=26.09 E-value=51 Score=37.64 Aligned_cols=56 Identities=25% Similarity=0.654 Sum_probs=37.2
Q ss_pred CCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCcceeecCCCC
Q 014105 238 CDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCM 316 (430)
Q Consensus 238 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~IeK~~GCn 316 (430)
|+--|... ..+.+-|-| .|+...|..|- ++ . .+...+-||+|+.+..+-.|++
T Consensus 21 CGd~vg~~-~~Ge~FVAC~eC~fpvCr~cy-ey---------e---------------~~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 21 CGDEVGVK-EDGQPFVACHVCGFPVCKPCY-EY---------E---------------RSEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred cccccCcC-CCCCEEEEeccCCCccccchh-hh---------h---------------hhcCCccCCccCCchhhhcCCC
Confidence 65555443 345677999 89999998885 11 1 1122388999999988666776
Q ss_pred ceE
Q 014105 317 HMT 319 (430)
Q Consensus 317 hm~ 319 (430)
.+.
T Consensus 75 ~~~ 77 (1044)
T PLN02915 75 RVE 77 (1044)
T ss_pred Ccc
Confidence 554
No 293
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=26.02 E-value=90 Score=22.48 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=25.2
Q ss_pred HHHHHHhHcCCCHHHHHHHHHhcCCChhhh
Q 014105 82 DITRISTVLSISKVAASILLRFYNWSVSKV 111 (430)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l 111 (430)
.+.+|+..|+++......=...++|+...-
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~ 44 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLP 44 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCc
Confidence 467899999999999888889999986543
No 294
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.84 E-value=49 Score=36.22 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=22.8
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc----ccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE----FCWLCLG 334 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~----FCw~C~~ 334 (430)
-+||+|..++.--.+=+.+.|. .||+. .|-.|+.
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch-~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCR-WCGRAAPDWRCPRCGS 430 (665)
T ss_pred eECCCCCCceeEecCCCeeECC-CCcCCCcCccCCCCcC
Confidence 4788888777654445678888 78864 3556654
No 295
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=25.82 E-value=33 Score=33.37 Aligned_cols=29 Identities=38% Similarity=0.831 Sum_probs=18.6
Q ss_pred CCCCCCCCcceeecCCCCceEecC-CCcccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLG 334 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~-~C~~~FCw~C~~ 334 (430)
..-|-+|..+|- ++=+. .|++.||+.|-.
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr 119 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECAR 119 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhh
Confidence 357999999986 22221 477777777753
No 296
>PLN02189 cellulose synthase
Probab=25.81 E-value=58 Score=37.17 Aligned_cols=50 Identities=30% Similarity=0.794 Sum_probs=34.5
Q ss_pred CCccccccccccccC----CCeeecc-CCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPS----DRLLAAA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~----~~~~~l~-CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.....|.||.+++.. +.++... |+-..|+.|. +|-.. +|. -.|| .|+...
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~---eg~----q~Cp--qCkt~Y 86 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERR---EGT----QNCP--QCKTRY 86 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---cCC----ccCc--ccCCch
Confidence 345589999998653 2344454 8999999999 55443 453 4799 788764
No 297
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.47 E-value=55 Score=35.99 Aligned_cols=35 Identities=20% Similarity=0.610 Sum_probs=25.5
Q ss_pred CCCCCCCcceeecCCCCceEecCCCccc-----cccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (430)
-.||+|..++.--..=+.+.|. .||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCH-HCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECC-CCcCCCCCCCCCCCCcCC
Confidence 3688888887633334678998 89986 58888764
No 298
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.31 E-value=54 Score=24.70 Aligned_cols=44 Identities=32% Similarity=0.818 Sum_probs=29.9
Q ss_pred ccccccccccCCCeeeccC--CCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 143 TCGICFENYPSDRLLAAAC--GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~C--gH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
.|..|-.+++....-.+-| .|.||.+|...-+. | .|| .|+..+.
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-----g------~CP--nCGGelv 52 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLH-----G------LCP--NCGGELV 52 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-----C------cCC--CCCchhh
Confidence 4888887777654444445 47899999875442 2 588 7887653
No 299
>PLN02436 cellulose synthase A
Probab=25.22 E-value=57 Score=37.32 Aligned_cols=60 Identities=23% Similarity=0.650 Sum_probs=39.9
Q ss_pred ecCCCCCCceEEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCCCccee
Q 014105 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (430)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C~~~Ie 310 (430)
-|.- |+--|... ..+..-|-| .|++..|..|- + +. .+..++.||+|++...
T Consensus 38 iCqI--CGD~Vg~t-~dGe~FVACn~C~fpvCr~Cy-e---------ye---------------r~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 38 TCQI--CGDEIELT-VDGEPFVACNECAFPVCRPCY-E---------YE---------------RREGNQACPQCKTRYK 89 (1094)
T ss_pred cccc--cccccCcC-CCCCEEEeeccCCCccccchh-h---------hh---------------hhcCCccCcccCCchh
Confidence 4553 66555444 345677999 89999998885 1 11 0122388999999998
Q ss_pred ecCCCCceE
Q 014105 311 KNQGCMHMT 319 (430)
Q Consensus 311 K~~GCnhm~ 319 (430)
+--|++.+.
T Consensus 90 r~kgs~~~~ 98 (1094)
T PLN02436 90 RIKGSPRVE 98 (1094)
T ss_pred hccCCCCcC
Confidence 777777654
No 300
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=25.09 E-value=1.8e+02 Score=27.33 Aligned_cols=24 Identities=33% Similarity=0.834 Sum_probs=18.9
Q ss_pred CCCCceEecCCCc----cccccccccccc
Q 014105 313 QGCMHMTCTPPCK----FEFCWLCLGQWS 337 (430)
Q Consensus 313 ~GCnhm~C~~~C~----~~FCw~C~~~~~ 337 (430)
..|.||.|. .|- ..+|.+|.+...
T Consensus 21 TaC~HvfC~-~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 21 TACRHVFCE-PCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eechhhhhh-hhcccCCccccccccceee
Confidence 679999998 554 459999998753
No 301
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=24.70 E-value=51 Score=28.65 Aligned_cols=66 Identities=12% Similarity=0.232 Sum_probs=38.2
Q ss_pred hcCCChhhhhhhhhhcHHHHHHHhCCCCCCCcCCCC----CCcccccccccccc--CCCeeeccCC-CcccHHHHHH
Q 014105 103 FYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPD----GEEMTCGICFENYP--SDRLLAAACG-HPFCSSCWTG 172 (430)
Q Consensus 103 ~~~W~~~~l~~~~~~~~~~~~~~~gl~~~~~~~~~~----~~~~~C~IC~e~~~--~~~~~~l~Cg-H~fC~~Cl~~ 172 (430)
.=-|+.+.+.++ ..+.+++.||-+......+. .....||-|-.... .+.+-++.|. ..+|++|..-
T Consensus 67 ~p~Wt~d~it~~----gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 67 DPPWTTDWITED----AREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CCCCChHHCCHH----HHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 445887776653 23345566875543221111 12478999987543 2344556787 5689999764
No 302
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=24.48 E-value=43 Score=21.65 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=13.3
Q ss_pred CCCCCCCCcceee-cCCCCceEecCCCcc
Q 014105 299 SKPCPRCKRPIEK-NQGCMHMTCTPPCKF 326 (430)
Q Consensus 299 tk~CP~C~~~IeK-~~GCnhm~C~~~C~~ 326 (430)
.-+||.|+...-. +.| ..+|. .||+
T Consensus 8 ~~~C~~C~~~~~~~~dG--~~yC~-~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDG--FYYCD-RCGH 33 (36)
T ss_pred CCcCCCCCCeEeEccCC--EEEhh-hCce
Confidence 3468888776432 233 35554 3554
No 303
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=24.22 E-value=65 Score=24.36 Aligned_cols=27 Identities=22% Similarity=0.770 Sum_probs=20.0
Q ss_pred CCCCCCCcc----eeecCCCCceEecCCCccc
Q 014105 300 KPCPRCKRP----IEKNQGCMHMTCTPPCKFE 327 (430)
Q Consensus 300 k~CP~C~~~----IeK~~GCnhm~C~~~C~~~ 327 (430)
-.||+|+.+ +-+..|=.++.|. .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV-~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECV-ECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-CCCCe
Confidence 479999864 2355778889999 78875
No 304
>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=24.17 E-value=60 Score=31.52 Aligned_cols=10 Identities=30% Similarity=1.065 Sum_probs=3.9
Q ss_pred ceecCCCCCCce
Q 014105 230 TKWCPAPGCDYA 241 (430)
Q Consensus 230 ~~~CP~p~C~~~ 241 (430)
..+||. |+..
T Consensus 172 ~g~CPv--CGs~ 181 (290)
T PF04216_consen 172 RGYCPV--CGSP 181 (290)
T ss_dssp -SS-TT--T---
T ss_pred CCcCCC--CCCc
Confidence 368996 8754
No 305
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=24.17 E-value=74 Score=36.50 Aligned_cols=50 Identities=32% Similarity=0.834 Sum_probs=34.2
Q ss_pred CCccccccccccccCC---C-eeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCc
Q 014105 139 GEEMTCGICFENYPSD---R-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~---~-~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l 198 (430)
.....|.||-+++..+ + ++.. .|+-..|+.|. +|=. ++|. -.|| .|+...
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr---~eG~----q~CP--qCktrY 69 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER---KDGN----QSCP--QCKTKY 69 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh---hcCC----ccCC--ccCCch
Confidence 3455899999987542 2 3444 38899999999 4433 3553 4799 788764
No 306
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.02 E-value=85 Score=25.75 Aligned_cols=11 Identities=55% Similarity=0.631 Sum_probs=5.8
Q ss_pred CcCcCCCCCCC
Q 014105 19 DDFYSGGDDDA 29 (430)
Q Consensus 19 ~~~~~~~~~~~ 29 (430)
||--+||.+-+
T Consensus 77 D~d~~GgDDlp 87 (129)
T COG4530 77 DDDPKGGDDLP 87 (129)
T ss_pred cCCccCCCccc
Confidence 45556655443
No 307
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=24.00 E-value=43 Score=32.82 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=22.7
Q ss_pred CceecCCCCCCceEEeecCCCCceEEecCCCccccccCC
Q 014105 229 KTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTE 267 (430)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~ 267 (430)
.+.-||. |...+. .+..+|.=|+..|..|..
T Consensus 47 ~lleCPv--C~~~l~------~Pi~QC~nGHlaCssC~~ 77 (299)
T KOG3002|consen 47 DLLDCPV--CFNPLS------PPIFQCDNGHLACSSCRT 77 (299)
T ss_pred hhccCch--hhccCc------ccceecCCCcEehhhhhh
Confidence 4567885 876543 467888888899998874
No 308
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.91 E-value=44 Score=35.67 Aligned_cols=30 Identities=23% Similarity=0.634 Sum_probs=25.9
Q ss_pred cCCCCCC--CCcceeecCCCCceEecCCCcccc
Q 014105 298 NSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 298 ~tk~CP~--C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
+...||+ |+..+.+...=+|..|. .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~-~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCE-KCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCC-CCCCcc
Confidence 4478995 99999999999999998 898776
No 309
>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 COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=23.68 E-value=69 Score=32.08 Aligned_cols=11 Identities=45% Similarity=1.367 Sum_probs=9.6
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
+.||-|+.|+.
T Consensus 335 QTCPICr~p~i 345 (491)
T COG5243 335 QTCPICRRPVI 345 (491)
T ss_pred cCCCcccCccc
Confidence 78999999964
No 311
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.61 E-value=27 Score=38.75 Aligned_cols=32 Identities=22% Similarity=0.527 Sum_probs=0.0
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCccc-----cccccccccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQWS 337 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~~~ 337 (430)
.++||+|+...- ..+|. .||.. +|..|+....
T Consensus 655 ~r~Cp~Cg~~t~------~~~Cp-~CG~~T~~~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 655 RRRCPKCGKETF------YNRCP-ECGSHTEPVYVCPDCGIEVE 691 (900)
T ss_dssp --------------------------------------------
T ss_pred cccCcccCCcch------hhcCc-ccCCccccceeccccccccC
Confidence 479999997753 36787 78877 8999987654
No 312
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.54 E-value=28 Score=30.29 Aligned_cols=9 Identities=56% Similarity=0.781 Sum_probs=4.5
Q ss_pred ccccccccc
Q 014105 141 EMTCGICFE 149 (430)
Q Consensus 141 ~~~C~IC~e 149 (430)
..+|||=-+
T Consensus 126 Eg~CPIVIe 134 (167)
T PF05320_consen 126 EGTCPIVIE 134 (167)
T ss_pred cCCCcEEEe
Confidence 445665443
No 313
>PF14353 CpXC: CpXC protein
Probab=23.15 E-value=44 Score=28.01 Aligned_cols=46 Identities=22% Similarity=0.478 Sum_probs=26.6
Q ss_pred cccCCCCCCCCchhhHHHhh---cChHHHHHHHHHHHHHHHhcCCCceecCCCCCCceEEe
Q 014105 187 LRCPDPSCGAAVGQDMIYLL---SSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (430)
Q Consensus 187 i~CP~~~C~~~l~~~~i~~l---l~~e~~~ky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~ 244 (430)
|+|| .|+..+.......+ ..+++.++ .+...-....||. |+..+..
T Consensus 2 itCP--~C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP~--Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCP--HCGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCPS--CGHKFRL 50 (128)
T ss_pred cCCC--CCCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECCC--CCCceec
Confidence 6899 89998765544333 33333332 2233345678885 8876543
No 314
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.02 E-value=54 Score=21.55 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=11.0
Q ss_pred ceEecCCCccccccc
Q 014105 317 HMTCTPPCKFEFCWL 331 (430)
Q Consensus 317 hm~C~~~C~~~FCw~ 331 (430)
-+.|. .|+..||-.
T Consensus 12 ~f~C~-~C~~~FC~~ 25 (39)
T smart00154 12 GFKCR-HCGNLFCGE 25 (39)
T ss_pred CeECC-ccCCccccc
Confidence 47888 799999854
No 315
>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=22.97 E-value=28 Score=24.03 Aligned_cols=44 Identities=30% Similarity=0.686 Sum_probs=21.5
Q ss_pred cccccccccccCCCeeeccC-CCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCchh
Q 014105 142 MTCGICFENYPSDRLLAAAC-GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (430)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~C-gH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~~ 200 (430)
+.|.-|.-.. .. .+.| .|+.|..|+...+.. .-.|| -|+.++|.
T Consensus 3 ~nCKsCWf~~--k~--Li~C~dHYLCl~CLt~ml~~---------s~~C~--iC~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN--KG--LIKCSDHYLCLNCLTLMLSR---------SDRCP--ICGKPLPT 47 (50)
T ss_dssp ----SS-S----SS--EEE-SS-EEEHHHHHHT-SS---------SSEET--TTTEE---
T ss_pred ccChhhhhcC--CC--eeeecchhHHHHHHHHHhcc---------ccCCC--cccCcCcc
Confidence 4577776321 22 3456 599999999887754 23688 78877654
No 316
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=22.56 E-value=62 Score=35.61 Aligned_cols=41 Identities=12% Similarity=0.159 Sum_probs=27.0
Q ss_pred ccccccccccccC--CCeeecc---CCCcccHHHHHHHHHhhhcCC
Q 014105 141 EMTCGICFENYPS--DRLLAAA---CGHPFCSSCWTGYISTAINDG 181 (430)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~---CgH~fC~~Cl~~yi~~~i~~g 181 (430)
..+|.+|.-.+.. +..-.++ |+|.+|-.||..+....+...
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~ 141 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESE 141 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccc
Confidence 4456666554432 1223334 999999999999998776543
No 317
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=22.56 E-value=1.1e+02 Score=22.17 Aligned_cols=29 Identities=21% Similarity=0.499 Sum_probs=19.7
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCccc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFC 262 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC 262 (430)
+.|| +|.+....- +.....|.| .|+...+
T Consensus 12 VkCp--~C~n~q~vF-sha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVF-SHASTVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEE-ecCCcEEECcccCCCcc
Confidence 5788 598765433 334577889 8988776
No 318
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.50 E-value=99 Score=30.46 Aligned_cols=39 Identities=28% Similarity=0.644 Sum_probs=0.0
Q ss_pred ecCCCCCCce-----EEeecCCCCceEEe-cCCCccccccCCcCCCCCCchhHHHHHHhhhhhHHHHHHHHhcCCCCCCC
Q 014105 232 WCPAPGCDYA-----VDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRC 305 (430)
Q Consensus 232 ~CP~p~C~~~-----i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~e~~~~~~i~~~tk~CP~C 305 (430)
+||. |+.. +......+.....| .|++ +||... -.||.|
T Consensus 189 ~CPv--CGs~P~~s~v~~~~~~G~RyL~CslC~t--------eW~~~R--------------------------~~C~~C 232 (309)
T PRK03564 189 FCPV--CGSMPVSSVVQIGTTQGLRYLHCNLCES--------EWHVVR--------------------------VKCSNC 232 (309)
T ss_pred CCCC--CCCcchhheeeccCCCCceEEEcCCCCC--------cccccC--------------------------ccCCCC
Q ss_pred C
Q 014105 306 K 306 (430)
Q Consensus 306 ~ 306 (430)
+
T Consensus 233 g 233 (309)
T PRK03564 233 E 233 (309)
T ss_pred C
No 319
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=22.44 E-value=30 Score=34.77 Aligned_cols=35 Identities=31% Similarity=0.893 Sum_probs=27.3
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHH
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGY 173 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y 173 (430)
..+.+|+|||-.++...-...-|.-.+|..|+..+
T Consensus 72 rr~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNLVRCCSETICGECFAPF 106 (482)
T ss_pred cccccCceeeeecccccchhhhhccchhhhheecc
Confidence 35688999998887544455569999999999765
No 320
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=22.44 E-value=1.7e+02 Score=24.36 Aligned_cols=35 Identities=20% Similarity=0.136 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhHcCCCHHHHHHHHHhcCCChhhhh
Q 014105 78 RQEEDITRISTVLSISKVAASILLRFYNWSVSKVH 112 (430)
Q Consensus 78 ~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~ 112 (430)
.=.++|.-|++..++|...|+-.|...+|++-..+
T Consensus 77 i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI 111 (116)
T TIGR00264 77 ITEDDIELVMKQCNVSKEEARRALEECGGDLAEAI 111 (116)
T ss_pred CCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHH
Confidence 34678889999999999999999999999975543
No 321
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=22.40 E-value=1.1e+02 Score=21.94 Aligned_cols=30 Identities=23% Similarity=0.491 Sum_probs=17.3
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCcccc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (430)
+.|| +|...-..- ......|.| .|+...|.
T Consensus 8 VkCp--~C~~~q~vF-Sha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVF-SHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEE-TT-SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEE-ecCCeEEEcccCCCEecC
Confidence 5788 598764443 345678999 89998874
No 322
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=21.86 E-value=2.1e+02 Score=23.83 Aligned_cols=34 Identities=24% Similarity=0.190 Sum_probs=29.4
Q ss_pred HHHHHHHHHhHcCCCHHHHHHHHHhcCCChhhhh
Q 014105 79 QEEDITRISTVLSISKVAASILLRFYNWSVSKVH 112 (430)
Q Consensus 79 ~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~ 112 (430)
=.++|.-|++..++|...|+-.|...+|++-..+
T Consensus 76 ~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI 109 (115)
T PRK06369 76 PEEDIELVAEQTGVSEEEARKALEEANGDLAEAI 109 (115)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHH
Confidence 3577888999999999999999999999976544
No 323
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.69 E-value=52 Score=27.92 Aligned_cols=11 Identities=45% Similarity=0.963 Sum_probs=8.4
Q ss_pred CCCCCCCccee
Q 014105 300 KPCPRCKRPIE 310 (430)
Q Consensus 300 k~CP~C~~~Ie 310 (430)
|.||+|+.-|-
T Consensus 111 K~C~~C~tGiY 121 (128)
T PF11682_consen 111 KYCPKCGTGIY 121 (128)
T ss_pred EecCCCCCccc
Confidence 78888887664
No 324
>PF15387 DUF4611: Domain of unknown function (DUF4611)
Probab=21.67 E-value=78 Score=25.16 Aligned_cols=14 Identities=57% Similarity=0.717 Sum_probs=7.3
Q ss_pred CCCCCCCCCCcccc
Q 014105 30 APAYAFDSDDADVA 43 (430)
Q Consensus 30 ~~~~~~~~~~~~~~ 43 (430)
.++++++++|+||+
T Consensus 61 ~p~E~ldg~dedda 74 (96)
T PF15387_consen 61 APDEALDGDDEDDA 74 (96)
T ss_pred CchhhccCcccccc
Confidence 34555565555544
No 325
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=21.64 E-value=31 Score=39.92 Aligned_cols=39 Identities=23% Similarity=0.545 Sum_probs=30.2
Q ss_pred CCccccccccccccCCCeeeccCCCcccHHHHHHHHHhhh
Q 014105 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAI 178 (430)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~yi~~~i 178 (430)
...+.|+||.+.+. ..-....|||.+|..|...+...+.
T Consensus 1151 ~~~~~c~ic~dil~-~~~~I~~cgh~~c~~c~~~~l~~~s 1189 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILR-NQGGIAGCGHEPCCRCDELWLYASS 1189 (1394)
T ss_pred hcccchHHHHHHHH-hcCCeeeechhHhhhHHHHHHHHhc
Confidence 35678999998763 2334567999999999999998743
No 326
>PF14369 zf-RING_3: zinc-finger
Probab=21.62 E-value=93 Score=19.94 Aligned_cols=28 Identities=36% Similarity=0.869 Sum_probs=16.8
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCcc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (430)
-||-. |...|...+. ....+.| .|+..|
T Consensus 3 ywCh~--C~~~V~~~~~-~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCHQ--CNRFVRIAPS-PDSDVACPRCHGGF 31 (35)
T ss_pred EeCcc--CCCEeEeCcC-CCCCcCCcCCCCcE
Confidence 58885 9988876532 2233456 666543
No 327
>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=21.44 E-value=45 Score=32.36 Aligned_cols=35 Identities=29% Similarity=0.686 Sum_probs=17.1
Q ss_pred CCCCCCCcce-----eecC--CCCceEecCCCcccc------ccccccc
Q 014105 300 KPCPRCKRPI-----EKNQ--GCMHMTCTPPCKFEF------CWLCLGQ 335 (430)
Q Consensus 300 k~CP~C~~~I-----eK~~--GCnhm~C~~~C~~~F------Cw~C~~~ 335 (430)
-.||-||.+- ...+ |=-+++|+ .|+++| |-.|+..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs-~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCS-LCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEET-TT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcC-CCCCeeeecCCCCcCCCCC
Confidence 6899999752 2333 78999998 899876 7788754
No 328
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=21.32 E-value=87 Score=34.24 Aligned_cols=22 Identities=18% Similarity=0.351 Sum_probs=15.3
Q ss_pred hcChHHHHHHHHHHHHHHHhcC
Q 014105 206 LSSDEDKVKYNRYFIRSYVEDN 227 (430)
Q Consensus 206 ll~~e~~~ky~~~~~~~~v~~~ 227 (430)
-++...+++|+.+.++-|....
T Consensus 1088 ~l~~a~kq~ye~La~~iFsk~~ 1109 (1189)
T KOG2041|consen 1088 ELDDAEKQEYENLAFRIFSKNP 1109 (1189)
T ss_pred hCCHHHHHHHHHHHHHHhccCC
Confidence 3456677888888887765543
No 329
>PRK11426 hypothetical protein; Provisional
Probab=21.03 E-value=1.5e+02 Score=25.37 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=32.3
Q ss_pred EEecHHHHHHHHH-HHHHHHHhHcCCCHHHHHHHHHhc
Q 014105 68 TVLTEADIRQRQE-EDITRISTVLSISKVAASILLRFY 104 (430)
Q Consensus 68 ~~l~~~~i~~~~~-~~i~~v~~~l~i~~~~a~~LL~~~ 104 (430)
..+++++|.+.+- +.|.+++.-+++++.++...|-.+
T Consensus 59 ~pIs~~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA~~ 96 (132)
T PRK11426 59 QSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQ 96 (132)
T ss_pred CCCCHHHHHHHhChHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 5679999999886 789999999999999999888654
No 330
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=20.96 E-value=60 Score=25.80 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=22.6
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
.-.||.|+..-.|..+----.|. +|+..|
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~-~C~~~~ 63 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCR-KCGAKF 63 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcC-CCCCEE
Confidence 36899998887777777777888 687765
No 331
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.89 E-value=59 Score=25.80 Aligned_cols=29 Identities=34% Similarity=0.724 Sum_probs=22.9
Q ss_pred CCCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 299 tk~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
.-.||.|+..-.|..+----.|. +|+..|
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~-~C~~~~ 64 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECR-KCGAKF 64 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcC-CCCCEE
Confidence 36899999888777777777888 687765
No 332
>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]
Probab=20.77 E-value=2.4e+02 Score=29.65 Aligned_cols=12 Identities=25% Similarity=-0.061 Sum_probs=9.6
Q ss_pred CCcccccccccc
Q 014105 323 PCKFEFCWLCLG 334 (430)
Q Consensus 323 ~C~~~FCw~C~~ 334 (430)
.|.+.||-+|..
T Consensus 559 ~klt~~~~lk~r 570 (653)
T KOG2548|consen 559 PKLTFFECLKSR 570 (653)
T ss_pred CcccHHHHHHHH
Confidence 488889988875
No 333
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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 domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=20.72 E-value=34 Score=21.24 Aligned_cols=18 Identities=28% Similarity=0.667 Sum_probs=9.1
Q ss_pred ecccCCCCCCCCchhhHH
Q 014105 186 MLRCPDPSCGAAVGQDMI 203 (430)
Q Consensus 186 ~i~CP~~~C~~~l~~~~i 203 (430)
.++||...|...+.....
T Consensus 2 ~vrCPvkdC~EEv~lgKY 19 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKY 19 (30)
T ss_dssp EEE--STT---EEEHHHH
T ss_pred ccccccccCcchhhhhhh
Confidence 589999999987755433
No 334
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.71 E-value=62 Score=39.23 Aligned_cols=28 Identities=32% Similarity=0.879 Sum_probs=23.7
Q ss_pred CCCCCCCcc------eeecCCCCceEecCCCcccccc
Q 014105 300 KPCPRCKRP------IEKNQGCMHMTCTPPCKFEFCW 330 (430)
Q Consensus 300 k~CP~C~~~------IeK~~GCnhm~C~~~C~~~FCw 330 (430)
..||.|+.. +...+||. +|. .||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~-~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCP-VCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCC-CCCCcccc
Confidence 349999999 78899997 898 89987774
No 335
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.59 E-value=99 Score=35.41 Aligned_cols=52 Identities=27% Similarity=0.789 Sum_probs=34.8
Q ss_pred CCCccccccccccccCC---C-eeec-cCCCcccHHHHHHHHHhhhcCCCceeecccCCCCCCCCch
Q 014105 138 DGEEMTCGICFENYPSD---R-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (430)
Q Consensus 138 ~~~~~~C~IC~e~~~~~---~-~~~l-~CgH~fC~~Cl~~yi~~~i~~g~~~~~i~CP~~~C~~~l~ 199 (430)
+.....|.||-+.+..+ + ++.. .|+-..|+.|. +|= .++|. -.|| .|+....
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye---~~~g~----~~cp--~c~t~y~ 68 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYE---RSEGN----QCCP--QCNTRYK 68 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhh---hhcCC----ccCC--ccCCchh
Confidence 33566899999986542 3 3444 38889999999 443 33453 4799 7887653
No 336
>PLN00209 ribosomal protein S27; Provisional
Probab=20.59 E-value=1.1e+02 Score=23.90 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=21.1
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCcccc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (430)
+-|| +|...-.+- +.....|.| .|+...|.
T Consensus 37 VkCp--~C~n~q~VF-ShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVF-SHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEE-ecCceEEEccccCCEeec
Confidence 6788 598754433 345678899 89998874
No 337
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.52 E-value=68 Score=28.17 Aligned_cols=27 Identities=19% Similarity=0.627 Sum_probs=19.2
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (430)
..||+|++.+...+. ....|. .|+..+
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~-~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCE-KCNKSV 61 (166)
T ss_pred ccccccCcccEeCCC-CcEECC-CCCCcC
Confidence 679999988876653 557777 677653
No 338
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=20.40 E-value=1.1e+02 Score=23.84 Aligned_cols=30 Identities=30% Similarity=0.691 Sum_probs=21.2
Q ss_pred eecCCCCCCceEEeecCCCCceEEe-cCCCcccc
Q 014105 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (430)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (430)
+-|| +|...-.+- +.....|.| .|+...|.
T Consensus 36 VkCp--~C~n~q~VF-ShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVF-SHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEE-ecCceEEEccccCCEeec
Confidence 6788 598754433 345678899 89998884
No 339
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.13 E-value=79 Score=22.96 Aligned_cols=32 Identities=19% Similarity=0.559 Sum_probs=19.9
Q ss_pred CCCCCCCcceeecCCCCceEecCCCcccccccc
Q 014105 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLC 332 (430)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C 332 (430)
..|-.|++.|.-.+..-+..|. .||...=|+|
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CP-nCG~~~I~RC 39 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCP-NCGEVIIYRC 39 (59)
T ss_pred ccccCCCCcccCCCccCEeeCC-CCCCeeEeec
Confidence 3567777777655556677776 6776644444
Done!