Query 019929
Match_columns 334
No_of_seqs 327 out of 1492
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 05:39:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 2.7E-34 5.9E-39 274.9 8.4 184 147-334 144-331 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 3.1E-32 6.6E-37 252.1 9.5 186 145-333 180-393 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 8.2E-30 1.8E-34 250.1 13.3 235 77-334 14-254 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 9.2E-24 2E-28 189.5 7.7 181 146-334 218-425 (446)
5 smart00647 IBR In Between Ring 99.3 4.4E-12 9.5E-17 91.0 4.9 63 220-282 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 5.1E-12 1.1E-16 90.6 1.8 63 220-282 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.5 4.7E-08 1E-12 64.0 2.4 41 152-198 1-41 (42)
8 PF13639 zf-RING_2: Ring finge 98.4 1.3E-07 2.8E-12 62.5 2.7 41 151-198 2-42 (44)
9 PF13923 zf-C3HC4_2: Zinc fing 98.4 2.1E-07 4.5E-12 59.9 3.3 38 152-198 1-38 (39)
10 PF00097 zf-C3HC4: Zinc finger 98.4 3.4E-07 7.5E-12 59.4 3.2 40 152-198 1-40 (41)
11 PF13445 zf-RING_UBOX: RING-ty 98.3 6E-07 1.3E-11 58.8 2.9 42 152-197 1-43 (43)
12 PLN03208 E3 ubiquitin-protein 98.2 1.4E-06 3E-11 75.3 4.5 64 147-215 16-88 (193)
13 PF14634 zf-RING_5: zinc-RING 98.2 1E-06 2.2E-11 58.3 2.7 41 151-198 1-41 (44)
14 KOG0320 Predicted E3 ubiquitin 98.2 1.2E-06 2.5E-11 74.0 3.5 57 146-212 128-184 (187)
15 cd00162 RING RING-finger (Real 98.1 3.7E-06 8E-11 54.9 3.5 44 151-204 1-44 (45)
16 KOG2177 Predicted E3 ubiquitin 98.0 3.4E-06 7.4E-11 78.0 2.7 111 146-284 10-124 (386)
17 PF13920 zf-C3HC4_3: Zinc fing 97.9 1.2E-05 2.6E-10 54.6 3.2 46 149-206 2-48 (50)
18 PHA02926 zinc finger-like prot 97.8 2E-05 4.2E-10 69.1 3.3 57 147-206 168-230 (242)
19 KOG0823 Predicted E3 ubiquitin 97.7 2.5E-05 5.4E-10 68.8 3.2 60 146-214 44-103 (230)
20 KOG2164 Predicted E3 ubiquitin 97.7 2.1E-05 4.6E-10 76.5 2.5 60 149-215 186-245 (513)
21 smart00184 RING Ring finger. E 97.6 4E-05 8.7E-10 48.0 2.7 30 152-184 1-30 (39)
22 PHA02929 N1R/p28-like protein; 97.6 4.1E-05 8.9E-10 68.9 3.6 51 147-206 172-227 (238)
23 smart00504 Ubox Modified RING 97.6 7.4E-05 1.6E-09 53.0 4.0 51 150-212 2-52 (63)
24 TIGR00599 rad18 DNA repair pro 97.5 8.9E-05 1.9E-09 71.5 3.9 67 146-224 23-90 (397)
25 COG5540 RING-finger-containing 97.4 0.00014 3E-09 66.4 3.4 53 147-207 321-373 (374)
26 KOG0317 Predicted E3 ubiquitin 97.3 0.00015 3.2E-09 65.9 3.2 53 146-210 236-288 (293)
27 TIGR00570 cdk7 CDK-activating 97.3 0.00035 7.6E-09 64.9 5.1 54 150-212 4-60 (309)
28 KOG0978 E3 ubiquitin ligase in 97.2 0.00059 1.3E-08 69.6 5.8 55 148-213 642-696 (698)
29 KOG0287 Postreplication repair 97.2 0.00019 4.1E-09 66.4 1.8 65 147-223 21-86 (442)
30 PF11789 zf-Nse: Zinc-finger o 97.0 0.00073 1.6E-08 47.1 3.1 48 148-202 10-57 (57)
31 KOG4628 Predicted E3 ubiquitin 97.0 0.00045 9.7E-09 65.2 2.7 49 150-206 230-278 (348)
32 PF12678 zf-rbx1: RING-H2 zinc 96.7 0.0018 4E-08 47.5 3.3 42 150-198 20-71 (73)
33 COG5574 PEX10 RING-finger-cont 96.3 0.0021 4.5E-08 57.9 2.1 53 148-210 214-266 (271)
34 PF14835 zf-RING_6: zf-RING of 96.3 0.0007 1.5E-08 47.8 -0.8 50 149-211 7-56 (65)
35 PF04564 U-box: U-box domain; 96.2 0.0051 1.1E-07 45.1 3.3 52 148-210 3-54 (73)
36 smart00647 IBR In Between Ring 96.1 0.0089 1.9E-07 42.1 4.0 36 299-334 7-48 (64)
37 KOG1002 Nucleotide excision re 96.0 0.0047 1E-07 60.5 2.7 57 146-209 533-589 (791)
38 PF11793 FANCL_C: FANCL C-term 95.8 0.0035 7.6E-08 45.6 0.9 58 149-208 2-68 (70)
39 COG5243 HRD1 HRD ubiquitin lig 95.3 0.054 1.2E-06 51.1 6.9 53 147-208 285-347 (491)
40 KOG1039 Predicted E3 ubiquitin 95.0 0.014 3.1E-07 55.3 2.2 58 147-206 159-221 (344)
41 KOG2879 Predicted E3 ubiquitin 94.9 0.031 6.7E-07 50.7 4.0 56 142-206 232-287 (298)
42 COG5432 RAD18 RING-finger-cont 94.5 0.025 5.3E-07 51.7 2.3 65 147-223 23-88 (391)
43 KOG4185 Predicted E3 ubiquitin 94.4 0.078 1.7E-06 49.5 5.7 122 149-280 3-131 (296)
44 KOG1812 Predicted E3 ubiquitin 94.4 0.0083 1.8E-07 58.2 -1.0 42 234-280 304-345 (384)
45 KOG0006 E3 ubiquitin-protein l 94.3 0.041 8.9E-07 50.8 3.4 95 169-278 341-437 (446)
46 KOG2660 Locus-specific chromos 94.3 0.022 4.9E-07 52.9 1.7 50 147-207 13-62 (331)
47 KOG0828 Predicted E3 ubiquitin 93.9 0.032 7E-07 54.4 2.0 56 143-206 565-634 (636)
48 PF01485 IBR: IBR domain; Int 93.8 0.025 5.3E-07 39.8 0.8 29 306-334 15-48 (64)
49 KOG1428 Inhibitor of type V ad 93.5 0.095 2.1E-06 57.2 4.7 66 149-216 3486-3554(3738)
50 PF14570 zf-RING_4: RING/Ubox 93.4 0.048 1E-06 36.4 1.7 46 152-205 1-47 (48)
51 PF12861 zf-Apc11: Anaphase-pr 93.1 0.084 1.8E-06 39.7 2.7 52 149-206 21-82 (85)
52 KOG0311 Predicted E3 ubiquitin 92.9 0.015 3.3E-07 54.5 -1.8 48 147-204 41-88 (381)
53 KOG0297 TNF receptor-associate 92.8 0.068 1.5E-06 52.1 2.4 50 146-206 18-67 (391)
54 KOG0802 E3 ubiquitin ligase [P 92.7 0.073 1.6E-06 54.1 2.5 48 147-201 289-338 (543)
55 KOG1814 Predicted E3 ubiquitin 92.4 0.093 2E-06 50.3 2.5 110 149-276 273-404 (445)
56 PF05883 Baculo_RING: Baculovi 92.3 0.069 1.5E-06 43.6 1.4 37 148-184 25-67 (134)
57 COG5152 Uncharacterized conser 92.2 0.05 1.1E-06 47.0 0.5 33 149-184 196-228 (259)
58 KOG4739 Uncharacterized protei 92.1 0.063 1.4E-06 48.0 1.0 50 149-210 3-52 (233)
59 KOG4367 Predicted Zn-finger pr 92.1 0.12 2.7E-06 49.7 3.0 35 147-184 2-36 (699)
60 KOG1785 Tyrosine kinase negati 91.6 0.065 1.4E-06 51.0 0.6 46 149-202 369-414 (563)
61 KOG4265 Predicted E3 ubiquitin 91.5 0.21 4.5E-06 47.2 3.8 50 146-207 287-337 (349)
62 KOG0824 Predicted E3 ubiquitin 91.5 0.088 1.9E-06 48.5 1.3 53 149-212 7-59 (324)
63 PF09788 Tmemb_55A: Transmembr 90.9 0.12 2.6E-06 46.6 1.5 75 147-251 63-138 (256)
64 smart00661 RPOL9 RNA polymeras 90.7 0.16 3.4E-06 34.3 1.7 25 310-334 1-28 (52)
65 KOG2817 Predicted E3 ubiquitin 90.5 0.31 6.7E-06 46.6 4.0 60 147-212 332-391 (394)
66 PF13719 zinc_ribbon_5: zinc-r 90.5 0.18 4E-06 31.7 1.7 30 237-268 3-35 (37)
67 smart00744 RINGv The RING-vari 90.5 0.36 7.7E-06 32.4 3.2 42 151-198 1-47 (49)
68 KOG4159 Predicted E3 ubiquitin 90.0 0.27 5.9E-06 47.7 3.3 49 147-207 82-130 (398)
69 COG5220 TFB3 Cdk activating ki 89.8 0.071 1.5E-06 47.4 -0.8 51 150-206 11-64 (314)
70 PF04641 Rtf2: Rtf2 RING-finge 89.5 0.6 1.3E-05 42.9 5.0 69 146-224 110-180 (260)
71 KOG1645 RING-finger-containing 89.4 0.26 5.5E-06 47.3 2.4 53 149-208 4-58 (463)
72 KOG1952 Transcription factor N 89.0 0.37 7.9E-06 50.3 3.4 54 147-202 189-243 (950)
73 KOG4692 Predicted E3 ubiquitin 88.9 0.38 8.3E-06 45.3 3.2 37 146-185 419-455 (489)
74 PHA00626 hypothetical protein 88.6 0.31 6.8E-06 33.3 1.8 24 311-334 2-31 (59)
75 PRK00432 30S ribosomal protein 88.4 0.29 6.2E-06 33.1 1.5 25 308-334 19-45 (50)
76 KOG0825 PHD Zn-finger protein 88.3 0.51 1.1E-05 48.9 3.8 51 149-208 123-173 (1134)
77 KOG0827 Predicted E3 ubiquitin 88.2 0.23 5E-06 47.3 1.3 48 149-202 4-52 (465)
78 COG5175 MOT2 Transcriptional r 87.3 0.48 1E-05 44.4 2.8 57 148-212 13-70 (480)
79 PF10571 UPF0547: Uncharacteri 87.2 0.34 7.4E-06 28.0 1.1 23 238-268 2-24 (26)
80 PF13717 zinc_ribbon_4: zinc-r 86.9 0.47 1E-05 29.6 1.8 30 237-268 3-35 (36)
81 KOG1734 Predicted RING-contain 86.9 0.22 4.8E-06 45.2 0.3 56 148-210 223-285 (328)
82 PF10367 Vps39_2: Vacuolar sor 85.7 2.5 5.3E-05 32.7 5.8 33 147-180 76-108 (109)
83 KOG0826 Predicted E3 ubiquitin 85.4 3.9 8.4E-05 38.4 7.6 48 148-204 299-346 (357)
84 KOG3039 Uncharacterized conser 85.2 0.8 1.7E-05 41.1 2.9 57 147-212 219-276 (303)
85 KOG4445 Uncharacterized conser 85.0 0.63 1.4E-05 43.0 2.3 42 146-187 112-153 (368)
86 smart00661 RPOL9 RNA polymeras 84.7 0.67 1.5E-05 31.1 1.8 28 238-267 2-29 (52)
87 KOG2034 Vacuolar sorting prote 84.7 1.9 4E-05 45.5 5.8 41 145-186 813-853 (911)
88 PF02150 RNA_POL_M_15KD: RNA p 84.5 0.45 9.7E-06 29.6 0.8 28 237-267 2-29 (35)
89 COG5222 Uncharacterized conser 84.4 1.5 3.2E-05 40.6 4.3 45 149-203 274-318 (427)
90 KOG3800 Predicted E3 ubiquitin 83.6 1.4 2.9E-05 40.6 3.8 52 151-210 2-55 (300)
91 KOG1815 Predicted E3 ubiquitin 83.5 1.1 2.4E-05 44.5 3.5 45 236-284 226-277 (444)
92 PF09297 zf-NADH-PPase: NADH p 83.5 1.2 2.7E-05 26.8 2.4 27 308-334 2-29 (32)
93 PRK00398 rpoP DNA-directed RNA 83.1 1.1 2.4E-05 29.4 2.3 25 310-334 4-29 (46)
94 PHA03096 p28-like protein; Pro 83.1 0.66 1.4E-05 43.1 1.6 39 150-188 179-222 (284)
95 PRK14714 DNA polymerase II lar 82.8 0.98 2.1E-05 49.4 3.0 29 237-275 668-701 (1337)
96 COG1998 RPS31 Ribosomal protei 82.7 0.75 1.6E-05 30.7 1.3 26 309-334 19-45 (51)
97 PF14803 Nudix_N_2: Nudix N-te 82.3 0.8 1.7E-05 28.3 1.3 25 310-334 1-30 (34)
98 PRK08665 ribonucleotide-diphos 81.3 0.77 1.7E-05 48.6 1.6 23 310-334 725-748 (752)
99 KOG0804 Cytoplasmic Zn-finger 81.2 1.1 2.3E-05 43.7 2.3 39 146-184 172-211 (493)
100 KOG1001 Helicase-like transcri 80.9 0.55 1.2E-05 48.9 0.3 52 150-212 455-506 (674)
101 KOG4172 Predicted E3 ubiquitin 79.8 0.5 1.1E-05 32.2 -0.3 45 150-205 8-53 (62)
102 PRK04023 DNA polymerase II lar 79.6 1.3 2.9E-05 47.3 2.6 32 236-277 626-662 (1121)
103 TIGR02098 MJ0042_CXXC MJ0042 f 79.5 1.1 2.4E-05 28.0 1.3 30 237-268 3-35 (38)
104 PF14447 Prok-RING_4: Prokaryo 79.0 0.75 1.6E-05 31.5 0.4 47 149-209 7-53 (55)
105 PF02318 FYVE_2: FYVE-type zin 79.0 6.2 0.00014 31.6 5.8 34 148-181 53-88 (118)
106 COG5219 Uncharacterized conser 78.2 2.4 5.3E-05 45.1 3.9 53 147-206 1467-1523(1525)
107 KOG1813 Predicted E3 ubiquitin 77.3 0.74 1.6E-05 42.4 -0.0 46 149-206 241-286 (313)
108 PRK14559 putative protein seri 76.6 1.4 3.1E-05 45.6 1.8 14 307-320 39-52 (645)
109 COG2888 Predicted Zn-ribbon RN 75.9 1.4 3.1E-05 30.6 1.0 25 310-334 28-58 (61)
110 PRK14890 putative Zn-ribbon RN 75.2 2.9 6.2E-05 29.1 2.4 26 238-267 9-34 (59)
111 COG5236 Uncharacterized conser 74.6 5.9 0.00013 37.5 5.1 69 145-223 57-125 (493)
112 TIGR00570 cdk7 CDK-activating 73.3 2.7 5.8E-05 39.4 2.5 53 238-323 5-57 (309)
113 COG1198 PriA Primosomal protei 72.6 7.2 0.00016 41.1 5.7 11 308-318 474-484 (730)
114 PF01599 Ribosomal_S27: Riboso 72.5 2.5 5.5E-05 28.1 1.6 27 308-334 17-46 (47)
115 COG1645 Uncharacterized Zn-fin 72.3 2.2 4.8E-05 34.8 1.5 25 308-334 27-52 (131)
116 PLN03086 PRLI-interacting fact 72.1 9.6 0.00021 38.9 6.3 97 193-333 407-548 (567)
117 PRK00420 hypothetical protein; 72.0 2.4 5.2E-05 33.7 1.7 24 308-333 22-47 (112)
118 KOG0823 Predicted E3 ubiquitin 71.6 1.3 2.9E-05 39.4 0.1 37 257-321 60-96 (230)
119 PF12677 DUF3797: Domain of un 71.3 2.9 6.4E-05 27.8 1.6 26 309-334 13-46 (49)
120 KOG3002 Zn finger protein [Gen 70.8 2.6 5.7E-05 39.5 1.9 47 146-206 45-91 (299)
121 KOG0978 E3 ubiquitin ligase in 70.7 1 2.2E-05 46.6 -0.9 30 262-319 659-688 (698)
122 TIGR02443 conserved hypothetic 70.6 3.7 7.9E-05 28.6 2.1 25 310-334 10-39 (59)
123 KOG0320 Predicted E3 ubiquitin 70.4 1.1 2.5E-05 38.2 -0.5 31 262-321 149-179 (187)
124 PF07282 OrfB_Zn_ribbon: Putat 70.3 2.9 6.3E-05 29.8 1.7 27 308-334 27-54 (69)
125 PF06677 Auto_anti-p27: Sjogre 69.3 4 8.7E-05 26.3 1.9 23 309-333 17-41 (41)
126 KOG2807 RNA polymerase II tran 69.2 0.96 2.1E-05 42.3 -1.3 83 172-277 276-364 (378)
127 PF12773 DZR: Double zinc ribb 68.5 3.9 8.5E-05 27.1 1.9 10 307-316 41-50 (50)
128 PRK00398 rpoP DNA-directed RNA 68.5 4.8 0.0001 26.4 2.3 28 237-268 4-31 (46)
129 PRK14873 primosome assembly pr 68.0 9.1 0.0002 40.0 5.3 23 256-278 381-406 (665)
130 KOG1941 Acetylcholine receptor 67.0 1.7 3.7E-05 41.6 -0.2 50 148-204 364-414 (518)
131 PF13240 zinc_ribbon_2: zinc-r 66.6 2.9 6.2E-05 23.3 0.7 22 238-267 1-22 (23)
132 PF09526 DUF2387: Probable met 66.2 4.8 0.0001 29.3 2.1 25 310-334 9-38 (71)
133 PF14569 zf-UDP: Zinc-binding 65.9 4.1 8.9E-05 30.0 1.6 44 256-327 26-69 (80)
134 PF14952 zf-tcix: Putative tre 65.7 3.3 7.1E-05 26.9 1.0 22 306-331 8-29 (44)
135 TIGR03655 anti_R_Lar restricti 65.6 4.3 9.2E-05 27.6 1.6 25 310-334 2-34 (53)
136 KOG2906 RNA polymerase III sub 65.3 4.7 0.0001 31.0 1.9 29 237-267 2-30 (105)
137 PF03119 DNA_ligase_ZBD: NAD-d 65.1 6.4 0.00014 23.1 2.1 21 311-331 1-21 (28)
138 PF08274 PhnA_Zn_Ribbon: PhnA 65.0 3.2 6.8E-05 24.9 0.8 24 310-334 3-27 (30)
139 smart00659 RPOLCX RNA polymera 63.7 5.8 0.00013 25.9 1.9 13 308-320 18-30 (44)
140 PF03604 DNA_RNApol_7kD: DNA d 63.7 4.1 8.8E-05 24.8 1.1 12 308-319 16-27 (32)
141 KOG0801 Predicted E3 ubiquitin 63.1 2.9 6.2E-05 35.2 0.5 29 147-175 175-203 (205)
142 PF14445 Prok-RING_2: Prokaryo 63.0 1.1 2.4E-05 30.0 -1.6 36 148-183 6-41 (57)
143 PF13248 zf-ribbon_3: zinc-rib 62.7 3.9 8.4E-05 23.4 0.8 23 237-267 3-25 (26)
144 PRK04023 DNA polymerase II lar 62.2 5.1 0.00011 43.1 2.2 27 258-284 626-656 (1121)
145 COG5109 Uncharacterized conser 62.1 11 0.00025 35.2 4.2 57 146-208 333-389 (396)
146 PF14149 YhfH: YhfH-like prote 61.8 1.1 2.3E-05 28.2 -1.7 28 303-330 7-34 (37)
147 PRK14892 putative transcriptio 60.8 6 0.00013 30.8 1.8 28 307-334 19-50 (99)
148 PLN03208 E3 ubiquitin-protein 60.7 6.8 0.00015 34.2 2.4 65 234-321 16-80 (193)
149 PF08746 zf-RING-like: RING-li 60.5 4.6 0.0001 26.2 1.0 41 152-197 1-41 (43)
150 COG1594 RPB9 DNA-directed RNA 60.3 6 0.00013 31.5 1.8 29 237-267 3-31 (113)
151 KOG4275 Predicted E3 ubiquitin 59.4 8.1 0.00017 35.8 2.7 31 149-182 300-331 (350)
152 PHA02926 zinc finger-like prot 59.2 2.2 4.8E-05 38.0 -0.9 76 216-321 155-231 (242)
153 KOG0317 Predicted E3 ubiquitin 59.0 4.6 9.9E-05 37.3 1.1 17 259-275 252-268 (293)
154 PF05290 Baculo_IE-1: Baculovi 58.3 23 0.00049 29.0 4.8 53 148-206 79-132 (140)
155 PF14446 Prok-RING_1: Prokaryo 58.1 10 0.00022 26.0 2.4 33 149-181 5-38 (54)
156 PRK14714 DNA polymerase II lar 57.8 6.5 0.00014 43.4 2.1 50 258-320 667-720 (1337)
157 KOG3579 Predicted E3 ubiquitin 57.3 9.8 0.00021 35.1 2.8 54 147-202 266-321 (352)
158 PF08271 TF_Zn_Ribbon: TFIIB z 56.8 9.4 0.0002 24.6 2.0 23 311-333 2-26 (43)
159 PF07754 DUF1610: Domain of un 56.7 7.6 0.00016 22.0 1.3 9 308-316 15-23 (24)
160 KOG2164 Predicted E3 ubiquitin 56.3 6.6 0.00014 39.1 1.7 35 263-321 203-237 (513)
161 PRK12286 rpmF 50S ribosomal pr 55.3 6.9 0.00015 27.1 1.2 24 306-334 24-48 (57)
162 PF07975 C1_4: TFIIH C1-like d 54.9 3.9 8.4E-05 27.7 -0.1 23 257-279 20-42 (51)
163 TIGR01206 lysW lysine biosynth 53.7 14 0.0003 25.3 2.5 30 237-268 3-32 (54)
164 CHL00174 accD acetyl-CoA carbo 53.6 3.3 7.1E-05 38.7 -0.8 26 309-334 38-65 (296)
165 PF06844 DUF1244: Protein of u 52.9 9.2 0.0002 27.2 1.5 17 173-189 11-27 (68)
166 PF01396 zf-C4_Topoisom: Topoi 52.8 13 0.00028 23.5 2.1 21 310-331 2-25 (39)
167 KOG3970 Predicted E3 ubiquitin 51.8 18 0.00039 32.2 3.5 54 150-206 51-105 (299)
168 PF14354 Lar_restr_allev: Rest 51.1 12 0.00025 25.9 1.9 25 309-333 3-36 (61)
169 KOG3161 Predicted E3 ubiquitin 50.6 5.3 0.00012 40.8 0.1 37 149-185 11-48 (861)
170 TIGR03826 YvyF flagellar opero 50.0 14 0.0003 30.5 2.4 14 308-321 80-93 (137)
171 PF06906 DUF1272: Protein of u 48.7 13 0.00029 25.5 1.8 45 150-206 6-52 (57)
172 KOG3039 Uncharacterized conser 48.7 13 0.00027 33.7 2.1 39 148-189 42-80 (303)
173 KOG1940 Zn-finger protein [Gen 48.6 7.9 0.00017 35.8 0.9 47 148-203 157-204 (276)
174 PF07800 DUF1644: Protein of u 48.3 26 0.00056 29.6 3.8 37 149-187 2-50 (162)
175 PRK14559 putative protein seri 48.0 13 0.00029 38.6 2.5 32 235-276 14-51 (645)
176 PF13453 zf-TFIIB: Transcripti 47.7 9.3 0.0002 24.3 0.9 27 238-266 1-27 (41)
177 KOG1493 Anaphase-promoting com 46.9 6.9 0.00015 28.7 0.2 50 150-205 21-80 (84)
178 PF14569 zf-UDP: Zinc-binding 46.8 26 0.00055 25.9 3.1 51 148-206 8-62 (80)
179 PF12906 RINGv: RING-variant d 46.8 16 0.00034 24.1 1.9 33 152-185 1-38 (47)
180 PF01428 zf-AN1: AN1-like Zinc 46.5 8 0.00017 25.0 0.4 18 258-275 13-30 (43)
181 PHA02929 N1R/p28-like protein; 45.9 13 0.00028 33.7 1.8 38 236-275 174-211 (238)
182 KOG3268 Predicted E3 ubiquitin 45.6 25 0.00053 30.2 3.3 59 147-207 163-229 (234)
183 KOG2114 Vacuolar assembly/sort 45.5 33 0.00072 36.5 4.8 42 148-203 839-880 (933)
184 PF02891 zf-MIZ: MIZ/SP-RING z 45.5 26 0.00056 23.5 2.8 47 150-203 3-49 (50)
185 PRK09521 exosome complex RNA-b 45.4 14 0.00031 32.1 1.9 24 310-334 150-174 (189)
186 PRK00420 hypothetical protein; 45.3 34 0.00074 27.2 3.9 44 217-267 6-49 (112)
187 PF00643 zf-B_box: B-box zinc 45.1 5.7 0.00012 25.2 -0.5 25 257-281 14-38 (42)
188 PRK08115 ribonucleotide-diphos 44.8 10 0.00022 40.6 1.1 22 310-333 828-851 (858)
189 PF14369 zf-RING_3: zinc-finge 44.7 27 0.00058 21.6 2.6 30 236-268 2-31 (35)
190 cd00021 BBOX B-Box-type zinc f 44.1 11 0.00023 23.2 0.7 25 257-281 11-35 (39)
191 KOG0309 Conserved WD40 repeat- 43.1 18 0.00039 37.9 2.4 47 148-203 1027-1073(1081)
192 COG1997 RPL43A Ribosomal prote 42.7 17 0.00038 27.4 1.7 27 308-334 34-61 (89)
193 PRK12495 hypothetical protein; 42.6 29 0.00062 30.9 3.3 12 236-249 42-53 (226)
194 PF06827 zf-FPG_IleRS: Zinc fi 42.4 13 0.00027 21.9 0.8 21 310-330 2-24 (30)
195 PF14471 DUF4428: Domain of un 42.2 24 0.00051 23.8 2.2 30 151-182 1-30 (51)
196 PF00098 zf-CCHC: Zinc knuckle 41.1 16 0.00034 19.0 0.9 16 268-283 2-17 (18)
197 PF03833 PolC_DP2: DNA polymer 40.7 9.1 0.0002 40.6 0.0 16 259-274 668-688 (900)
198 KOG2932 E3 ubiquitin ligase in 40.4 7.6 0.00017 36.2 -0.5 49 237-325 91-139 (389)
199 PF01363 FYVE: FYVE zinc finge 40.2 16 0.00035 25.8 1.2 37 147-183 7-44 (69)
200 PRK14892 putative transcriptio 40.2 26 0.00057 27.2 2.5 34 233-268 18-52 (99)
201 COG1579 Zn-ribbon protein, pos 39.5 21 0.00046 32.3 2.1 57 209-267 167-230 (239)
202 COG1996 RPC10 DNA-directed RNA 38.0 19 0.00041 24.1 1.2 15 306-320 21-35 (49)
203 smart00336 BBOX B-Box-type zin 37.6 20 0.00043 22.3 1.2 24 258-281 15-38 (42)
204 PF07191 zinc-ribbons_6: zinc- 37.5 24 0.00053 25.5 1.8 18 311-330 3-20 (70)
205 COG5151 SSL1 RNA polymerase II 37.3 5 0.00011 37.4 -2.2 87 171-275 307-405 (421)
206 KOG2807 RNA polymerase II tran 37.3 30 0.00066 32.6 2.8 42 152-202 333-374 (378)
207 COG3492 Uncharacterized protei 37.2 22 0.00048 27.0 1.6 17 173-189 42-58 (104)
208 PF12760 Zn_Tnp_IS1595: Transp 36.9 56 0.0012 21.2 3.4 25 310-334 19-45 (46)
209 PRK08332 ribonucleotide-diphos 36.9 19 0.00041 41.6 1.7 23 310-334 1705-1734(1740)
210 PF09538 FYDLN_acid: Protein o 36.8 22 0.00048 28.0 1.6 27 237-268 10-36 (108)
211 PRK00241 nudC NADH pyrophospha 36.7 31 0.00067 31.6 2.8 33 300-334 92-125 (256)
212 TIGR00373 conserved hypothetic 36.4 25 0.00054 29.7 2.0 30 235-267 108-137 (158)
213 smart00834 CxxC_CXXC_SSSS Puta 36.3 28 0.00061 21.7 1.8 28 237-266 6-34 (41)
214 KOG2907 RNA polymerase I trans 36.2 28 0.00062 27.5 2.1 18 193-212 25-42 (116)
215 smart00531 TFIIE Transcription 35.9 27 0.00058 29.0 2.1 32 234-267 97-132 (147)
216 PF02148 zf-UBP: Zn-finger in 34.7 42 0.00092 23.4 2.7 32 152-185 1-36 (63)
217 PF05605 zf-Di19: Drought indu 34.6 20 0.00044 24.2 1.0 40 149-205 2-41 (54)
218 PLN02638 cellulose synthase A 34.2 26 0.00057 38.4 2.1 57 243-328 22-78 (1079)
219 KOG1701 Focal adhesion adaptor 34.1 18 0.00038 35.3 0.8 68 256-333 380-459 (468)
220 PF04981 NMD3: NMD3 family ; 34.1 22 0.00048 32.0 1.4 10 309-318 35-44 (236)
221 PF11023 DUF2614: Protein of u 33.9 22 0.00049 28.1 1.2 22 258-279 69-98 (114)
222 COG1096 Predicted RNA-binding 33.7 27 0.00058 30.3 1.7 23 310-334 150-173 (188)
223 COG3813 Uncharacterized protei 33.4 31 0.00067 25.0 1.7 58 151-223 7-66 (84)
224 KOG3053 Uncharacterized conser 33.3 66 0.0014 29.4 4.2 55 147-204 18-80 (293)
225 COG3357 Predicted transcriptio 33.2 44 0.00096 25.4 2.6 12 204-215 18-29 (97)
226 PRK06266 transcription initiat 33.2 33 0.00072 29.6 2.3 30 235-267 116-145 (178)
227 PRK11827 hypothetical protein; 32.3 34 0.00075 24.0 1.8 25 309-333 8-33 (60)
228 cd00065 FYVE FYVE domain; Zinc 31.7 30 0.00065 23.3 1.5 36 150-185 3-39 (57)
229 PF03615 GCM: GCM motif protei 31.6 20 0.00044 29.2 0.6 21 308-334 81-105 (143)
230 PRK03824 hypA hydrogenase nick 31.4 70 0.0015 26.2 3.8 14 236-251 70-83 (135)
231 PF14205 Cys_rich_KTR: Cystein 31.4 42 0.00091 23.0 2.0 30 235-266 3-36 (55)
232 KOG4362 Transcriptional regula 30.3 13 0.00028 38.6 -0.9 56 148-212 20-75 (684)
233 PLN02189 cellulose synthase 29.9 39 0.00084 37.0 2.5 60 238-328 36-95 (1040)
234 PHA02825 LAP/PHD finger-like p 29.8 46 0.001 28.1 2.5 51 147-208 6-61 (162)
235 TIGR00686 phnA alkylphosphonat 29.6 30 0.00066 27.2 1.3 26 238-268 4-29 (109)
236 PF10122 Mu-like_Com: Mu-like 29.2 17 0.00038 24.5 -0.1 29 237-267 5-33 (51)
237 PF09889 DUF2116: Uncharacteri 29.0 23 0.0005 24.7 0.5 14 309-322 3-16 (59)
238 COG1645 Uncharacterized Zn-fin 28.8 32 0.0007 28.1 1.4 24 237-266 29-52 (131)
239 COG0266 Nei Formamidopyrimidin 28.4 39 0.00084 31.3 2.0 24 310-333 246-272 (273)
240 TIGR03037 anthran_nbaC 3-hydro 28.3 26 0.00057 29.7 0.8 19 299-317 141-159 (159)
241 smart00064 FYVE Protein presen 28.0 43 0.00093 23.5 1.8 37 149-185 10-47 (68)
242 TIGR00622 ssl1 transcription f 27.9 25 0.00054 28.0 0.6 40 237-278 56-101 (112)
243 PF09788 Tmemb_55A: Transmembr 27.8 33 0.00072 31.2 1.4 95 149-267 85-186 (256)
244 TIGR00595 priA primosomal prot 27.7 37 0.00081 34.3 1.9 25 310-334 223-248 (505)
245 KOG2932 E3 ubiquitin ligase in 27.7 30 0.00065 32.4 1.1 33 149-183 90-122 (389)
246 PRK09710 lar restriction allev 27.6 61 0.0013 23.0 2.4 32 235-267 5-36 (64)
247 PRK13264 3-hydroxyanthranilate 27.6 27 0.00058 30.1 0.8 23 299-321 147-169 (177)
248 PRK01103 formamidopyrimidine/5 27.5 42 0.00091 30.9 2.1 24 310-333 246-272 (274)
249 KOG2930 SCF ubiquitin ligase, 27.3 47 0.001 25.9 1.9 24 168-198 79-102 (114)
250 PRK10220 hypothetical protein; 26.9 42 0.00091 26.5 1.6 25 238-267 5-29 (111)
251 TIGR01384 TFS_arch transcripti 26.9 35 0.00076 26.3 1.3 24 238-267 2-25 (104)
252 TIGR00577 fpg formamidopyrimid 26.5 45 0.00097 30.8 2.1 23 310-332 246-271 (272)
253 PRK14810 formamidopyrimidine-D 26.1 45 0.00098 30.7 2.0 25 309-333 244-271 (272)
254 PF05129 Elf1: Transcription e 26.1 33 0.00071 25.5 0.9 27 308-334 21-54 (81)
255 PF01873 eIF-5_eIF-2B: Domain 25.9 59 0.0013 26.4 2.4 34 299-334 85-122 (125)
256 PRK14811 formamidopyrimidine-D 25.9 45 0.00097 30.8 1.9 25 309-333 235-262 (269)
257 PF00628 PHD: PHD-finger; Int 25.5 40 0.00087 22.1 1.2 34 151-184 1-34 (51)
258 PF14353 CpXC: CpXC protein 25.3 47 0.001 26.7 1.8 44 194-249 2-49 (128)
259 PF02318 FYVE_2: FYVE-type zin 25.3 98 0.0021 24.6 3.6 35 236-275 54-88 (118)
260 PF07295 DUF1451: Protein of u 25.2 36 0.00078 28.4 1.1 10 309-318 130-139 (146)
261 KOG2979 Protein involved in DN 25.2 1E+02 0.0022 28.2 3.9 48 149-203 176-223 (262)
262 COG2051 RPS27A Ribosomal prote 25.1 48 0.001 23.7 1.5 31 237-270 20-50 (67)
263 KOG2789 Putative Zn-finger pro 25.1 23 0.00049 34.3 -0.2 36 147-183 72-107 (482)
264 PRK13945 formamidopyrimidine-D 24.9 48 0.001 30.7 2.0 24 310-333 255-281 (282)
265 PF10764 Gin: Inhibitor of sig 24.7 55 0.0012 21.6 1.7 35 151-189 1-35 (46)
266 PRK10445 endonuclease VIII; Pr 24.6 51 0.0011 30.3 2.0 24 310-333 236-262 (263)
267 PF07503 zf-HYPF: HypF finger; 24.4 34 0.00073 21.2 0.6 31 174-206 1-32 (35)
268 KOG1039 Predicted E3 ubiquitin 24.3 27 0.00059 33.4 0.2 39 261-321 184-222 (344)
269 PF13913 zf-C2HC_2: zinc-finge 24.2 39 0.00085 19.0 0.8 10 259-268 3-12 (25)
270 COG2816 NPY1 NTP pyrophosphohy 24.2 68 0.0015 29.7 2.8 28 307-334 109-137 (279)
271 PF03884 DUF329: Domain of unk 24.1 37 0.0008 23.6 0.8 15 309-323 2-16 (57)
272 PLN00209 ribosomal protein S27 23.7 83 0.0018 23.7 2.6 32 237-271 37-68 (86)
273 PLN02400 cellulose synthase 23.6 44 0.00095 36.8 1.6 45 256-328 53-97 (1085)
274 PF11682 DUF3279: Protein of u 23.3 53 0.0012 26.8 1.7 16 310-325 111-126 (128)
275 KOG1571 Predicted E3 ubiquitin 23.2 40 0.00087 32.2 1.1 44 147-205 303-346 (355)
276 PF13834 DUF4193: Domain of un 22.8 31 0.00067 26.7 0.2 31 147-178 68-98 (99)
277 TIGR02300 FYDLN_acid conserved 22.1 62 0.0013 26.3 1.8 27 237-268 10-36 (129)
278 smart00249 PHD PHD zinc finger 22.0 63 0.0014 20.0 1.6 32 151-182 1-32 (47)
279 PF08273 Prim_Zn_Ribbon: Zinc- 21.9 43 0.00094 21.4 0.7 25 150-178 4-32 (40)
280 PRK11032 hypothetical protein; 21.9 45 0.00099 28.3 1.1 12 307-318 140-151 (160)
281 PRK02935 hypothetical protein; 21.8 53 0.0012 25.7 1.3 11 268-278 88-98 (110)
282 PRK06386 replication factor A; 21.7 40 0.00086 32.5 0.8 14 308-321 235-248 (358)
283 KOG3183 Predicted Zn-finger pr 21.6 29 0.00064 31.2 -0.1 118 149-283 8-138 (250)
284 TIGR01562 FdhE formate dehydro 21.6 60 0.0013 30.6 1.9 11 310-320 253-263 (305)
285 PF04236 Transp_Tc5_C: Tc5 tra 21.5 55 0.0012 23.2 1.3 31 235-274 26-56 (63)
286 COG5194 APC11 Component of SCF 21.5 90 0.0019 23.2 2.4 18 168-185 52-69 (88)
287 COG3809 Uncharacterized protei 21.5 64 0.0014 23.9 1.6 12 238-251 3-14 (88)
288 PLN02915 cellulose synthase A 21.5 61 0.0013 35.5 2.2 45 256-328 32-76 (1044)
289 KOG1100 Predicted E3 ubiquitin 21.0 48 0.001 29.4 1.1 27 152-181 161-188 (207)
290 PLN02638 cellulose synthase A 21.0 1.1E+02 0.0025 33.7 4.0 51 148-206 16-70 (1079)
291 TIGR00100 hypA hydrogenase nic 20.8 92 0.002 24.7 2.6 25 236-266 70-94 (115)
292 PF08792 A2L_zn_ribbon: A2L zi 20.7 75 0.0016 19.3 1.6 29 236-268 3-31 (33)
293 PF08209 Sgf11: Sgf11 (transcr 20.7 51 0.0011 20.1 0.8 13 309-321 4-16 (33)
294 PF09151 DUF1936: Domain of un 20.4 46 0.001 19.9 0.6 9 311-319 3-11 (36)
295 PRK05580 primosome assembly pr 20.3 62 0.0013 34.0 1.9 25 310-334 391-416 (679)
296 PF01927 Mut7-C: Mut7-C RNAse 20.3 1.4E+02 0.0029 24.7 3.6 31 236-268 91-134 (147)
297 PHA02325 hypothetical protein 20.3 53 0.0012 23.2 1.0 11 308-318 2-12 (72)
298 PF15135 UPF0515: Uncharacteri 20.2 1.1E+02 0.0023 28.0 3.1 30 216-247 92-121 (278)
299 PRK01110 rpmF 50S ribosomal pr 20.2 68 0.0015 22.4 1.5 23 307-334 25-47 (60)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.7e-34 Score=274.92 Aligned_cols=184 Identities=33% Similarity=0.813 Sum_probs=156.1
Q ss_pred ccccccccccccccC-CceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHH
Q 019929 147 YGPFVCEICAEQKTV-HKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAA 225 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~ 225 (334)
....+|.||+.+.+. .+++....|+|.||.+||++|++++. .+...+.||..+|+..++.+.+..+|++++.++|++.
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~-~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~ 222 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKL-LSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQR 222 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhh-ccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHH
Confidence 347899999955444 36666779999999999999999993 3446789999999999999999999999999999999
Q ss_pred HHHhhcCCCCcccCCCCCCCceEEcCCc---cccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHH
Q 019929 226 LCEAVIPGAQKFYCPFKDCSAMLIDDGE---EVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMK 302 (334)
Q Consensus 226 ~~~~~~~~~~~~~CP~p~C~~~~~~~~~---~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~ 302 (334)
+.+.++...+.+|||+|+|...+..... .......|+.|+..||..|+.+||.+.+|++|++|..++. .+..+.+
T Consensus 223 ~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~--~d~~~~~ 300 (384)
T KOG1812|consen 223 LKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEY--VDDITLK 300 (384)
T ss_pred HHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCccc--ccHHHHH
Confidence 9999988877779999999987765431 3445578999999999999999999999999999976443 3334444
Q ss_pred HHHhCCccccCCCCceeeeccCCCceEeecCC
Q 019929 303 VAQKEKWKRCPNCRYYVEKKDGCMYMKCRSVF 334 (334)
Q Consensus 303 ~~~~~~~k~CP~C~~~IeK~~GCnhMtC~Cg~ 334 (334)
++. ++|++||+|++.|++++|||||||+|||
T Consensus 301 ~la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~ 331 (384)
T KOG1812|consen 301 YLA-KRWRQCPKCKFMIELSEGCNHMTCRCGH 331 (384)
T ss_pred HHH-HhcCcCcccceeeeecCCcceEEeeccc
Confidence 443 8999999999999999999999999996
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.1e-32 Score=252.13 Aligned_cols=186 Identities=26% Similarity=0.642 Sum_probs=153.6
Q ss_pred CCccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCC-eeeeecCCCcCCCCCchhhhhccCChHHHHHHH
Q 019929 145 IVYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEEN-ITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWG 223 (334)
Q Consensus 145 ~~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~ 223 (334)
++...+.|.|||++..+...+..++|+|.||+.|++.|+...|.+| +..++||.++|+...++..++.+++.+++++|+
T Consensus 180 F~~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 180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 4566899999999998878888899999999999999999999998 588999999999999999999999999999999
Q ss_pred HHHHHhhcC-CCCcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhH--------HHHhh-hhh
Q 019929 224 AALCEAVIP-GAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEF--------QKLNK-DER 293 (334)
Q Consensus 224 ~~~~~~~~~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~--------~~~~~-~~~ 293 (334)
+++.+..+. .++.+|||++.|+.....+++ ...+.|.+|+..||+.|+..||....|..- ..|.. ++.
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 KLMLQKTLELMSDVVYCPRACCQLPVKQDPG--RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCccccCch--hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 988776665 567889999999998755444 345899999999999999999999999642 12221 110
Q ss_pred h----------------HHHHHHHHHHHhCCccccCCCCceeeeccCCCceEee-cC
Q 019929 294 E----------------REDILLMKVAQKEKWKRCPNCRYYVEKKDGCMYMKCR-SV 333 (334)
Q Consensus 294 ~----------------~~d~~~~~~~~~~~~k~CP~C~~~IeK~~GCnhMtC~-Cg 333 (334)
. .++.+..+|+ ..+.|+||+|+++|||++|||||+|. ||
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl-~~N~krCP~C~v~IEr~eGCnKM~C~~c~ 393 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWL-ESNSKRCPKCKVVIERSEGCNKMHCTKCG 393 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHH-HhcCCCCCcccceeecCCCccceeecccc
Confidence 0 0122233455 56889999999999999999999995 76
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=8.2e-30 Score=250.05 Aligned_cols=235 Identities=21% Similarity=0.424 Sum_probs=186.5
Q ss_pred cchhhhhhhhhhhhHHHHHHHhhhhhHHHHHHHHHHhhhhcHHHHHHHHhhhccccCCCCCCCCCCCCCCcccccccccc
Q 019929 77 GKMLQTEKPLNKHGDELAIVLEQLKSVENTMSFIDDRFGSLTESLTELKQRISTVPCKGSYASPPKSGIVYGPFVCEICA 156 (334)
Q Consensus 77 ~~~~~ve~~l~~~~~~~~~~L~~~~~~~~~~~~i~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~ 156 (334)
-++.++..+|+.......++|.++.|. ...++++++... +.......... .+ ......+|.||+
T Consensus 14 ~~i~~~~~~ls~~~~~~~~ll~~~~W~--~~kl~~~~~~~~-~~~~~~~g~~~----------~~---~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 14 EDIIEVSDILSLSHAVARILLAHFCWN--VEKLLEEWVEDE-ETGCFFVGLLL----------WP---KKKGDVQCGICV 77 (444)
T ss_pred hhHHHHHHhhcCCHHHHHHHHHhcCcc--hHHHHHHHHhcC-cchhhhccccc----------cC---CCCccccCCccc
Confidence 456788889999999999999999994 445566666543 33221111000 00 224468999999
Q ss_pred ccccCCceeEecCCCCcccHHHHHHHHHhhhhCCe-eeeecCCCcCCCCCchhhhhccCCh-HHHHHHHHHHHHhhcCCC
Q 019929 157 EQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENI-TAIRCPVVDCRGLLEPEYCRDILPQ-DVFDRWGAALCEAVIPGA 234 (334)
Q Consensus 157 e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~l~~~~i~~ll~~-~~~~~y~~~~~~~~~~~~ 234 (334)
+.++. . ...+.|+|.||..||..|+..+|.++. ..|+||..+|...+..+.|..++++ +..++|.+++...++...
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-E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 98765 3 445699999999999999999998863 3399999999999999999999988 599999999999988865
Q ss_pred C-cccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccC
Q 019929 235 Q-KFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCP 313 (334)
Q Consensus 235 ~-~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP 313 (334)
. +.|||+|+|+..+... ......+.| .|++.||+.|+.+||.|.+|.....|.+... ++....+|+ ..++++||
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~--~~se~~~wi-~~ntk~CP 230 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCR--DDSETINWI-LANTKECP 230 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhh--hhhhhhhhh-hccCccCC
Confidence 4 5699999999988763 233456899 5888999999999999999999999976554 344445576 68999999
Q ss_pred CCCceeeeccCCCceEee---cCC
Q 019929 314 NCRYYVEKKDGCMYMKCR---SVF 334 (334)
Q Consensus 314 ~C~~~IeK~~GCnhMtC~---Cg~ 334 (334)
+|.++|||++|||||+|. |+|
T Consensus 231 ~c~~~iek~~gc~~~~~~~~~c~~ 254 (444)
T KOG1815|consen 231 KCKVPIEKDGGCNHMTCKSASCKH 254 (444)
T ss_pred CcccchhccCCccccccccCCcCC
Confidence 999999999999999996 765
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=9.2e-24 Score=189.53 Aligned_cols=181 Identities=25% Similarity=0.550 Sum_probs=140.5
Q ss_pred CccccccccccccccCCceeEecCCC--CcccHHHHHHHHHhhhhCC--------eeeeecCCCcCCCCCchh-hhhccC
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCS--HAYCTDCMVKYVAAKLEEN--------ITAIRCPVVDCRGLLEPE-YCRDIL 214 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~--------~~~i~CP~~~C~~~l~~~-~i~~ll 214 (334)
+....+|..|-+.- +++-.++|. |..|.+|++.|..+++++. .+.+.||+ +|...+-.+ ....+|
T Consensus 218 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 218 NSRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred ccccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 45688999998743 344455898 9999999999999999763 26788997 888766554 345689
Q ss_pred ChHHHHHHHHHHHHhhcCCCCcccCCCCCCCceEEcCCccccccccCCc-cccccccccCccCCCCCCchhHH-------
Q 019929 215 PQDVFDRWGAALCEAVIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPN-CRRLFCAQCQVPWHSGINCVEFQ------- 286 (334)
Q Consensus 215 ~~~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~-C~~~fC~~C~~~~H~~~tC~~~~------- 286 (334)
..+.+.+|+++..+.++...+.+.||.|+|+..+.+.+. ...++|+. |++.||.+|...||.+ .|...-
T Consensus 294 g~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD--~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~t 370 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD--QRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTTT 370 (446)
T ss_pred chhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC--CCcccCCCCchhHhHHHHHhhhccc-cceeeeccccccc
Confidence 999999999999999888888999999999998887653 45699986 9999999999999998 343210
Q ss_pred -----HHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeeccCCCceEee---cCC
Q 019929 287 -----KLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKKDGCMYMKCR---SVF 334 (334)
Q Consensus 287 -----~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~~GCnhMtC~---Cg~ 334 (334)
..+..+..+.|.....-+ +..+|+||+|+++.||||||.||.|+ ||+
T Consensus 371 c~y~vde~~a~~arwd~as~~TI-k~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~ 425 (446)
T KOG0006|consen 371 CAYRVDERAAEQARWDAASKETI-KKTTKPCPKCHVPTERNGGCMHMKCTQPQCGL 425 (446)
T ss_pred eeeecChhhhhhhhhhhhhhhhh-hhccCCCCCccCccccCCceEEeecCCCCCCc
Confidence 111122223344444444 67899999999999999999999995 886
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.28 E-value=4.4e-12 Score=90.96 Aligned_cols=63 Identities=37% Similarity=0.852 Sum_probs=53.3
Q ss_pred HHHHHHHHHhhcCC-CCcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCc
Q 019929 220 DRWGAALCEAVIPG-AQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINC 282 (334)
Q Consensus 220 ~~y~~~~~~~~~~~-~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC 282 (334)
++|++++.+.++.. ...+|||+|+|+.++..........+.|+.|+..||+.|+.+||.|.+|
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 47888888888776 5667999999999888764334567999999999999999999999987
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=99.20 E-value=5.1e-12 Score=90.59 Aligned_cols=63 Identities=27% Similarity=0.735 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhcCCC-CcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCc
Q 019929 220 DRWGAALCEAVIPGA-QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINC 282 (334)
Q Consensus 220 ~~y~~~~~~~~~~~~-~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC 282 (334)
++|++++.+.++... ..+|||+|+|+.++..+.......+.|+.|++.||+.|+.+||.|.+|
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 468887777777654 446999999999998876654445999999999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.54 E-value=4.7e-08 Score=63.96 Aligned_cols=41 Identities=22% Similarity=0.719 Sum_probs=28.7
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
|+||++.+. +++++ +|||.||..|+..++...-.. .+.||.
T Consensus 1 CpiC~~~~~--~Pv~l-~CGH~FC~~Cl~~~~~~~~~~---~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFK--DPVSL-PCGHSFCRSCLERLWKEPSGS---GFSCPE 41 (42)
T ss_dssp ETTTTSB-S--SEEE--SSSSEEEHHHHHHHHCCSSSS---T---SS
T ss_pred CCccchhhC--Ccccc-CCcCHHHHHHHHHHHHccCCc---CCCCcC
Confidence 899999876 66765 999999999999999754322 278883
No 8
>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=98.44 E-value=1.3e-07 Score=62.51 Aligned_cols=41 Identities=24% Similarity=0.613 Sum_probs=33.1
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
+|+||++++...+.+..++|+|.||.+|+..|+... ..||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence 599999999766666666899999999999999763 28884
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=98.43 E-value=2.1e-07 Score=59.88 Aligned_cols=38 Identities=32% Similarity=1.002 Sum_probs=29.7
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
|+||++.+. +.+.+++|||.||.+||.+|++.. .+||.
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKN-------PKCPV 38 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence 899999866 565677999999999999998762 47884
No 10
>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=98.37 E-value=3.4e-07 Score=59.43 Aligned_cols=40 Identities=30% Similarity=0.910 Sum_probs=31.8
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
|+||++.+. +...+++|||.||..|+.+|+.. ...+.||.
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN-----SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH-----TSSSBTTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh-----cCCccCCc
Confidence 899999876 33456799999999999999987 13457883
No 11
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.29 E-value=6e-07 Score=58.82 Aligned_cols=42 Identities=29% Similarity=0.744 Sum_probs=22.9
Q ss_pred cccccccccC-CceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecC
Q 019929 152 CEICAEQKTV-HKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCP 197 (334)
Q Consensus 152 C~IC~e~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 197 (334)
|+||.+ +.. .+...+|+|||.||++|+.+++.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999 643 34445678999999999999998532 2467887
No 12
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.22 E-value=1.4e-06 Score=75.30 Aligned_cols=64 Identities=25% Similarity=0.528 Sum_probs=47.5
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhh---------CCeeeeecCCCcCCCCCchhhhhccCC
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLE---------ENITAIRCPVVDCRGLLEPEYCRDILP 215 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~i~CP~~~C~~~l~~~~i~~ll~ 215 (334)
.+.++|+||++.+. +.+. ..|||.||..|+..|+...-. .......|| .|...++...+..+..
T Consensus 16 ~~~~~CpICld~~~--dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiyg 88 (193)
T PLN03208 16 GGDFDCNICLDQVR--DPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYG 88 (193)
T ss_pred CCccCCccCCCcCC--CcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeec
Confidence 45799999999764 4454 589999999999999764211 112356899 6999999887776654
No 13
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.20 E-value=1e-06 Score=58.27 Aligned_cols=41 Identities=27% Similarity=0.830 Sum_probs=33.7
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
.|+||++.+.....+.+++|||.||..|+.... ...+.||.
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~ 41 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI 41 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC
Confidence 499999999555567788999999999999887 23678994
No 14
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=1.2e-06 Score=73.96 Aligned_cols=57 Identities=21% Similarity=0.651 Sum_probs=44.3
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
..+.+-|+||++.+.....++. .|||.||..|++..+.. ..+|| .|...|+..++..
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk~-------~~~CP--~C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALKN-------TNKCP--TCRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhhcccccc-ccchhHHHHHHHHHHHh-------CCCCC--Ccccccchhhhee
Confidence 3457999999999986665655 89999999999998875 45899 4666777665544
No 15
>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=98.08 E-value=3.7e-06 Score=54.88 Aligned_cols=44 Identities=30% Similarity=0.782 Sum_probs=33.7
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCC
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGL 204 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 204 (334)
+|+||++.+. +.+.+.+|+|.||..|+..|+.. ....|| .|+..
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence 4999999872 44556679999999999999875 245798 57654
No 16
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=3.4e-06 Score=77.96 Aligned_cols=111 Identities=19% Similarity=0.417 Sum_probs=67.2
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHH
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAA 225 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~ 225 (334)
..+.+.|+||++.+... .+++|+|.||+.|+..++. ..+.|| .|.. ... .+...-........
T Consensus 10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr~-~~~----~~~~n~~l~~~~~~ 72 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCRP-PSR----NLRPNVLLANLVER 72 (386)
T ss_pred ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccCC-chh----ccCccHHHHHHHHH
Confidence 34679999999998754 5679999999999999998 358999 5773 222 22222222222222
Q ss_pred HHHhhcCC-CCc--ccCCCCCCCceEEcCCccccccccCCccccccccccC-ccCCCCCCchh
Q 019929 226 LCEAVIPG-AQK--FYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQ-VPWHSGINCVE 284 (334)
Q Consensus 226 ~~~~~~~~-~~~--~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~-~~~H~~~tC~~ 284 (334)
+....... ... ..|+. .. ......|..|....|..|. ...|..+.-..
T Consensus 73 ~~~~~~~~~~~~~~~~c~~--~~---------~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~ 124 (386)
T KOG2177|consen 73 LRQLRLSRPLGSKEELCEK--HG---------EELKLFCEEDEKLLCVLCRESGEHRGHPVLP 124 (386)
T ss_pred HHhcCCcccccccchhhhh--cC---------CcceEEecccccccCCCCCCcccccCCcccc
Confidence 21111111 111 13331 11 1134789999999999998 66788775544
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=97.88 E-value=1.2e-05 Score=54.59 Aligned_cols=46 Identities=28% Similarity=0.739 Sum_probs=34.5
Q ss_pred ccccccccccccCCceeEecCCCCc-ccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHA-YCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
...|.||++... + +.+++|||. ||..|+..++.. ...|| -|...+.
T Consensus 2 ~~~C~iC~~~~~--~-~~~~pCgH~~~C~~C~~~~~~~-------~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--D-VVLLPCGHLCFCEECAERLLKR-------KKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--S-EEEETTCEEEEEHHHHHHHHHT-------TSBBT--TTTBB-S
T ss_pred cCCCccCCccCC--c-eEEeCCCChHHHHHHhHHhccc-------CCCCC--cCChhhc
Confidence 467999999744 4 445699999 999999999982 45899 5887664
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=97.76 E-value=2e-05 Score=69.08 Aligned_cols=57 Identities=25% Similarity=0.593 Sum_probs=40.3
Q ss_pred ccccccccccccccC-----Ccee-EecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 147 YGPFVCEICAEQKTV-----HKSF-HIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~-----~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
+...+|+||++..-. ...| .+.+|+|.||..|+..|...+-..| ..-.|| -|...+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP--iCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP--ICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC--CCcceee
Confidence 457899999997521 1223 3569999999999999998754333 234799 5877654
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=2.5e-05 Score=68.82 Aligned_cols=60 Identities=20% Similarity=0.560 Sum_probs=46.1
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccC
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDIL 214 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll 214 (334)
....|+|.||++.-. +++.. .|||.||-.||-+|+..+.. .-.|| -|+..++.+.|-.|.
T Consensus 44 ~~~~FdCNICLd~ak--dPVvT-lCGHLFCWpClyqWl~~~~~----~~~cP--VCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAK--DPVVT-LCGHLFCWPCLYQWLQTRPN----SKECP--VCKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccC--CCEEe-ecccceehHHHHHHHhhcCC----CeeCC--ccccccccceEEeee
Confidence 356899999999743 55544 79999999999999987653 23678 588888887665554
No 20
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=2.1e-05 Score=76.45 Aligned_cols=60 Identities=23% Similarity=0.553 Sum_probs=46.4
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCC
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILP 215 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~ 215 (334)
...||||++..+. ..+..|||.||..|+.+||...... ....|| -|...|...++..++-
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~--~~~~CP--iC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIK--GPCSCP--ICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhccc--CCccCC--chhhhccccceeeeee
Confidence 7899999997543 2245799999999999999987222 466899 6999998877766543
No 21
>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=97.65 E-value=4e-05 Score=48.02 Aligned_cols=30 Identities=33% Similarity=0.909 Sum_probs=24.3
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHH
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVA 184 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 184 (334)
|+||++.. .....++|+|.||..|+..|+.
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 2344569999999999999987
No 22
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.64 E-value=4.1e-05 Score=68.87 Aligned_cols=51 Identities=24% Similarity=0.550 Sum_probs=37.7
Q ss_pred ccccccccccccccCCc-----eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 147 YGPFVCEICAEQKTVHK-----SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
....+|+||++.+.... ...+.+|+|.||..|+..|... ...|| -|...+.
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 34689999999865432 1245689999999999999864 23799 5877655
No 23
>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=97.61 E-value=7.4e-05 Score=52.96 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=39.2
Q ss_pred cccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
+.|+||.+.+. +++. ++|||.||+.|+..|+.. ...|| -|+..++.+.+..
T Consensus 2 ~~Cpi~~~~~~--~Pv~-~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMK--DPVI-LPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCC--CCEE-CCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhcee
Confidence 67999999865 4454 599999999999999975 23799 4777776655443
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.49 E-value=8.9e-05 Score=71.46 Aligned_cols=67 Identities=21% Similarity=0.587 Sum_probs=47.6
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhh-ccCChHHHHHHHH
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCR-DILPQDVFDRWGA 224 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~ll~~~~~~~y~~ 224 (334)
....+.|+||++.+. .++ +++|||.||..|+..|+... ..|| .|...+....+. ..+-.++++.|..
T Consensus 23 Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~~-------~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 23 LDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSNQ-------PKCP--LCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred cccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhCC-------CCCC--CCCCccccccCccchHHHHHHHHHHH
Confidence 456789999999875 334 46999999999999998642 2799 698877765433 2333456666653
No 25
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.00014 Score=66.37 Aligned_cols=53 Identities=23% Similarity=0.609 Sum_probs=45.0
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCch
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEP 207 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 207 (334)
....+|.||+++|...+.+..++|.|.|.+.|+.+|+.. ...+|| -|...+++
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~------y~~~CP--vCrt~iPP 373 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG------YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh------hcccCC--ccCCCCCC
Confidence 456899999999987777777899999999999999963 456899 69988875
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.00015 Score=65.93 Aligned_cols=53 Identities=25% Similarity=0.705 Sum_probs=41.5
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
.....-|.+|++... + .+..+|||.||-.|+..|...+- .|| -|...+.+..+
T Consensus 236 ~~a~~kC~LCLe~~~--~-pSaTpCGHiFCWsCI~~w~~ek~-------eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 236 PEATRKCSLCLENRS--N-PSATPCGHIFCWSCILEWCSEKA-------ECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCCceEEEecCCC--C-CCcCcCcchHHHHHHHHHHcccc-------CCC--cccccCCCcce
Confidence 345689999999753 3 33569999999999999997643 399 69988887654
No 27
>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=97.29 E-value=0.00035 Score=64.87 Aligned_cols=54 Identities=22% Similarity=0.447 Sum_probs=39.0
Q ss_pred cccccccccccC-Cce--eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 150 FVCEICAEQKTV-HKS--FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 150 ~~C~IC~e~~~~-~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
..||+|..+... .++ +.. .|||.||..|+..+|.. + ...|| .|...+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~----~--~~~CP--~C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVR----G--SGSCP--ECDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcC----C--CCCCC--CCCCccchhhccc
Confidence 579999985332 222 323 79999999999998742 2 34899 7998888776554
No 28
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.17 E-value=0.00059 Score=69.62 Aligned_cols=55 Identities=20% Similarity=0.658 Sum_probs=44.2
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhcc
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDI 213 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~l 213 (334)
....|++|..... +.+ +..|+|.||..|++..+.++- =+|| .|+..|...+|..+
T Consensus 642 ~~LkCs~Cn~R~K--d~v-I~kC~H~FC~~Cvq~r~etRq------RKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTRWK--DAV-ITKCGHVFCEECVQTRYETRQ------RKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCchh--hHH-HHhcchHHHHHHHHHHHHHhc------CCCC--CCCCCCCccccccc
Confidence 4789999995432 444 458999999999999998753 3899 79999999888764
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.15 E-value=0.00019 Score=66.41 Aligned_cols=65 Identities=23% Similarity=0.568 Sum_probs=49.0
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc-cCChHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD-ILPQDVFDRWG 223 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-ll~~~~~~~y~ 223 (334)
...+-|.||++.|... + +.+|+|.||.-|++.|+.. ...|| .|...+....++. .+-.++++.|.
T Consensus 21 D~lLRC~IC~eyf~ip--~-itpCsHtfCSlCIR~~L~~-------~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP--M-ITPCSHTFCSLCIRKFLSY-------KPQCP--TCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCc--e-eccccchHHHHHHHHHhcc-------CCCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence 4467899999988743 2 4589999999999999975 44799 6988888887765 34456665554
No 30
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.99 E-value=0.00073 Score=47.10 Aligned_cols=48 Identities=23% Similarity=0.600 Sum_probs=32.1
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCC
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCR 202 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 202 (334)
-.+.|||-...+. +++....|+|.|-++.+.+|+ .+...+.||..+|.
T Consensus 10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 3688999998866 677767999999999999999 22346799998884
No 31
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00045 Score=65.19 Aligned_cols=49 Identities=27% Similarity=0.658 Sum_probs=41.0
Q ss_pred cccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
.+|.||+|+|...+.+..|+|.|.|...|+..|+... .-.||. |+..+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPv--CK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPV--CKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCC--CCCcCC
Confidence 6999999999998888889999999999999999763 236995 665433
No 32
>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=96.66 E-value=0.0018 Score=47.51 Aligned_cols=42 Identities=21% Similarity=0.541 Sum_probs=30.2
Q ss_pred cccccccccccC----------CceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 150 FVCEICAEQKTV----------HKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 150 ~~C~IC~e~~~~----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
-.|.||++.+.. .-.+....|||.|...|+.+|+..+ -.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence 459999998821 1234556899999999999999653 28884
No 33
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.33 E-value=0.0021 Score=57.90 Aligned_cols=53 Identities=25% Similarity=0.599 Sum_probs=38.4
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
..+.|.||++.. ..++..+|||.||..|+...+..+ ..-.|| -|.+...+..+
T Consensus 214 ~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKK-----KYEFCP--LCRAKVYPKKV 266 (271)
T ss_pred cccceeeeeccc---CCcccccccchhhHHHHHHHHHhh-----ccccCc--hhhhhccchhh
Confidence 368899999863 334567999999999999954332 233699 68887776655
No 34
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.32 E-value=0.0007 Score=47.79 Aligned_cols=50 Identities=22% Similarity=0.640 Sum_probs=23.2
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhh
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCR 211 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 211 (334)
..-|++|.+.+. +++.+..|.|.||..|+...+. -.|| -|..+....+++
T Consensus 7 lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS--
T ss_pred hcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHHHH
Confidence 466999999865 5666779999999999977443 1499 587766555543
No 35
>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=96.20 E-value=0.0051 Score=45.10 Aligned_cols=52 Identities=17% Similarity=0.301 Sum_probs=36.3
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
+.|.|+|+.+.+. +++.+ ++||.|++.++..|+.. ....||. ++..++...+
T Consensus 3 ~~f~CpIt~~lM~--dPVi~-~~G~tyer~~I~~~l~~------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMR--DPVIL-PSGHTYERSAIERWLEQ------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-S--SEEEE-TTSEEEEHHHHHHHHCT------TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHhh--CceeC-CcCCEEcHHHHHHHHHc------CCCCCCC--CCCcCCcccc
Confidence 4689999999765 66654 89999999999999976 2347894 6777776543
No 36
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=96.07 E-value=0.0089 Score=42.13 Aligned_cols=36 Identities=28% Similarity=0.661 Sum_probs=28.4
Q ss_pred HHHHHHHh-CCccccC--CCCceeeecc--CCCceEe-ecCC
Q 019929 299 LLMKVAQK-EKWKRCP--NCRYYVEKKD--GCMYMKC-RSVF 334 (334)
Q Consensus 299 ~~~~~~~~-~~~k~CP--~C~~~IeK~~--GCnhMtC-~Cg~ 334 (334)
++..++.. .+++.|| +|+..|+..+ |..+|+| .||+
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~ 48 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGF 48 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCC
Confidence 44444443 5789999 9999999975 9999999 6986
No 37
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.95 E-value=0.0047 Score=60.48 Aligned_cols=57 Identities=26% Similarity=0.678 Sum_probs=43.4
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhh
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEY 209 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 209 (334)
.....+|.+|-+.-. +.+. ..|.|.||+-|++.|+......+ .+.|| .|-..++.+.
T Consensus 533 nk~~~~C~lc~d~ae--d~i~-s~ChH~FCrlCi~eyv~~f~~~~--nvtCP--~C~i~LsiDl 589 (791)
T KOG1002|consen 533 NKGEVECGLCHDPAE--DYIE-SSCHHKFCRLCIKEYVESFMENN--NVTCP--VCHIGLSIDL 589 (791)
T ss_pred ccCceeecccCChhh--hhHh-hhhhHHHHHHHHHHHHHhhhccc--CCCCc--cccccccccc
Confidence 456899999988532 4443 48999999999999998866543 38999 6887776653
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.83 E-value=0.0035 Score=45.65 Aligned_cols=58 Identities=14% Similarity=0.322 Sum_probs=27.4
Q ss_pred cccccccccccc-CCce--eEe--cCCCCcccHHHHHHHHHhhhhCC----eeeeecCCCcCCCCCchh
Q 019929 149 PFVCEICAEQKT-VHKS--FHI--KGCSHAYCTDCMVKYVAAKLEEN----ITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 149 ~~~C~IC~e~~~-~~~~--~~~--~~C~H~fC~~Cl~~~~~~~i~~~----~~~i~CP~~~C~~~l~~~ 208 (334)
+.+|+||+.... ..+. ... ..|++.|...||.+|+...-... ...-.|| .|...|...
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeEe
Confidence 468999998764 2221 111 37889999999999998765432 2334799 698877653
No 39
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.054 Score=51.14 Aligned_cols=53 Identities=19% Similarity=0.446 Sum_probs=38.8
Q ss_pred cccccccccccc-ccCC---------ceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchh
Q 019929 147 YGPFVCEICAEQ-KTVH---------KSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 147 ~~~~~C~IC~e~-~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 208 (334)
...-.|.||+++ +... .....++|||.+...|++.|++.+ -.|| -|+.++-.+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCP--ICr~p~ifd 347 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCP--ICRRPVIFD 347 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCC--cccCccccc
Confidence 446789999998 3222 123457999999999999999863 3799 587765444
No 40
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.96 E-value=0.014 Score=55.32 Aligned_cols=58 Identities=28% Similarity=0.513 Sum_probs=39.9
Q ss_pred ccccccccccccccCCc-----eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 147 YGPFVCEICAEQKTVHK-----SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
....+|.||++...... .-.+.+|.|.||..|++.|-...-.+....-.|| .|.....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--cccCccc
Confidence 56799999999865332 2234679999999999999754433333445899 4765433
No 41
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.88 E-value=0.031 Score=50.73 Aligned_cols=56 Identities=25% Similarity=0.516 Sum_probs=40.8
Q ss_pred CCCCCccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 142 KSGIVYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 142 ~~~~~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
.+...+...+|++|-+.- .-++....|+|.||--|+..-.... ..+.|| .|+....
T Consensus 232 sss~~t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp--~Cg~~~~ 287 (298)
T KOG2879|consen 232 SSSTGTSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWD-----ASFTCP--LCGENVE 287 (298)
T ss_pred ccccccCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcch-----hhcccC--ccCCCCc
Confidence 334456689999998753 3456666799999999998876543 347999 6877655
No 42
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.48 E-value=0.025 Score=51.66 Aligned_cols=65 Identities=18% Similarity=0.423 Sum_probs=42.7
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc-cCChHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD-ILPQDVFDRWG 223 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-ll~~~~~~~y~ 223 (334)
....-|-||-+.+.. ....+|||.||.-|++.|+..+ -.|| -|...+-+..++. .+..++.+.|.
T Consensus 23 Ds~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~q-------p~CP--~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 23 DSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQ-------PFCP--VCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hhHHHhhhhhheeec---ceecccccchhHHHHHHHhcCC-------CCCc--cccccHHhhhcccchhHHHHHHhhh
Confidence 446789999887653 2245899999999999999753 3688 4765544443333 23344444443
No 43
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.39 E-value=0.078 Score=49.51 Aligned_cols=122 Identities=21% Similarity=0.441 Sum_probs=64.3
Q ss_pred ccccccccccccCCc---eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCC--CchhhhhccCCh-HHHHHH
Q 019929 149 PFVCEICAEQKTVHK---SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGL--LEPEYCRDILPQ-DVFDRW 222 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~---~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--l~~~~i~~ll~~-~~~~~y 222 (334)
...|.||-++|+..+ ....+.|||.+|..|+...+.. ..+.|| -|... ++...++.+-.. .+++..
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~------~~i~cp--fcR~~~~~~~~~~~~l~kNf~ll~~~ 74 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN------SRILCP--FCRETTEIPDGDVKSLQKNFALLQAI 74 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC------ceeecc--CCCCcccCCchhHhhhhhhHHHHHHH
Confidence 467999999987542 3345789999999999888754 456788 47766 444444443221 122222
Q ss_pred HHHHHHhhcCCCCcccCCCCCCCceEEcCCccccccccCCccccccccccCcc-CCCCC
Q 019929 223 GAALCEAVIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVP-WHSGI 280 (334)
Q Consensus 223 ~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~-~H~~~ 280 (334)
+.. ....+.......+| +.|..............-.|+.....+|..|... .|.++
T Consensus 75 ~~~-~~~~~~~~~~~~~~-~~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~~~~~~ 131 (296)
T KOG4185|consen 75 EHM-KKTTVEEKGEADSP-PKCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFGIHKGH 131 (296)
T ss_pred HHH-hcccccccCcccCC-cccccCcccccceeecCCCcchhhhhhhhhccchhhhhhh
Confidence 211 11111111222333 1255432221111111124566667788888764 34443
No 44
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.35 E-value=0.0083 Score=58.21 Aligned_cols=42 Identities=24% Similarity=0.583 Sum_probs=34.1
Q ss_pred CCcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCC
Q 019929 234 AQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGI 280 (334)
Q Consensus 234 ~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 280 (334)
..++.|| .|...+....+ .+.++|. |++.||+.|+.+|+.+.
T Consensus 304 ~~wr~Cp--kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCc--ccceeeeecCC--cceEEee-ccccchhhcCcchhhCC
Confidence 5567899 99988766544 7789997 99999999999986644
No 45
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.29 E-value=0.041 Score=50.83 Aligned_cols=95 Identities=23% Similarity=0.550 Sum_probs=55.7
Q ss_pred CCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHHHHHhhcCCCCcccCCCCCCCceE
Q 019929 169 GCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAALCEAVIPGAQKFYCPFKDCSAML 248 (334)
Q Consensus 169 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~~ 248 (334)
.||-.||+.|+..|-...-..+... . -...|...+++.. ..-.+|+....... ......|| .|....
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~a-s-~t~tc~y~vde~~-------a~~arwd~as~~TI--k~tTkpCP--kChvpt 407 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEA-S-GTTTCAYRVDERA-------AEQARWDAASKETI--KKTTKPCP--KCHVPT 407 (446)
T ss_pred CchhHhHHHHHhhhccccceeeecc-c-cccceeeecChhh-------hhhhhhhhhhhhhh--hhccCCCC--CccCcc
Confidence 4999999999999875432211000 0 0012444444322 22356665543321 23345788 887665
Q ss_pred EcCCccccccccCCc--cccccccccCccCCC
Q 019929 249 IDDGEEVIQESECPN--CRRLFCAQCQVPWHS 278 (334)
Q Consensus 249 ~~~~~~~~~~~~C~~--C~~~fC~~C~~~~H~ 278 (334)
..+. ....+.|+. |+..+|++|+-+|..
T Consensus 408 ErnG--GCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 408 ERNG--GCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ccCC--ceEEeecCCCCCCceeEeccCChhhh
Confidence 5543 245578865 999999999998854
No 46
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=94.27 E-value=0.022 Score=52.94 Aligned_cols=50 Identities=26% Similarity=0.721 Sum_probs=38.2
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCch
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEP 207 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 207 (334)
....+|.+|-..+.. .-.+..|-|.||+.||-.|+.. ...|| .|...+..
T Consensus 13 n~~itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~-------~~~CP--~C~i~ih~ 62 (331)
T KOG2660|consen 13 NPHITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEE-------SKYCP--TCDIVIHK 62 (331)
T ss_pred ccceehhhccceeec--chhHHHHHHHHHHHHHHHHHHH-------hccCC--ccceeccC
Confidence 447899999988763 3334589999999999999987 34899 57665554
No 47
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.89 E-value=0.032 Score=54.42 Aligned_cols=56 Identities=23% Similarity=0.640 Sum_probs=40.7
Q ss_pred CCCCccccccccccccccCCc--------------eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 143 SGIVYGPFVCEICAEQKTVHK--------------SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 143 ~~~~~~~~~C~IC~e~~~~~~--------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
.++.+....|.||+.+++... .+-+.+|.|.|.+.|+.+|+.. ..+.||. |..+++
T Consensus 565 ~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 565 EAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT------YKLICPV--CRCPLP 634 (636)
T ss_pred cchhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh------hcccCCc--cCCCCC
Confidence 344667889999998875321 1224599999999999999974 3578995 666655
No 48
>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=93.77 E-value=0.025 Score=39.78 Aligned_cols=29 Identities=38% Similarity=0.896 Sum_probs=18.1
Q ss_pred hCCccccCC--CCceeeeccCCCc--eEee-cCC
Q 019929 306 KEKWKRCPN--CRYYVEKKDGCMY--MKCR-SVF 334 (334)
Q Consensus 306 ~~~~k~CP~--C~~~IeK~~GCnh--MtC~-Cg~ 334 (334)
..+.+.||+ |...|++..|.++ |+|. ||+
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCS
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCC
Confidence 345689988 9999999999999 9997 986
No 49
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.49 E-value=0.095 Score=57.23 Aligned_cols=66 Identities=20% Similarity=0.406 Sum_probs=52.5
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCC---eeeeecCCCcCCCCCchhhhhccCCh
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEEN---ITAIRCPVVDCRGLLEPEYCRDILPQ 216 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~ll~~ 216 (334)
.-.|.|||.+--...+...+.|+|.|...|.+..++.+...- ...|.|| -|+.+|....++.+|++
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence 456899997654444455579999999999999998876542 3678999 69999999888888874
No 50
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.45 E-value=0.048 Score=36.39 Aligned_cols=46 Identities=26% Similarity=0.636 Sum_probs=20.9
Q ss_pred cccccccccCCc-eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCC
Q 019929 152 CEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLL 205 (334)
Q Consensus 152 C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 205 (334)
|++|.+++...+ .+.--+|++.+|+.||..-.+. + .=.|| +|+...
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 788998875433 2333489999999999876642 1 22799 687653
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.12 E-value=0.084 Score=39.69 Aligned_cols=52 Identities=25% Similarity=0.562 Sum_probs=34.7
Q ss_pred cccccccccccc---------CCc-eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 149 PFVCEICAEQKT---------VHK-SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 149 ~~~C~IC~e~~~---------~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
...|+||...|. +.+ ++..-.|+|.|...|+.+|+.++-. .-.|| -|.+.+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CP--mCR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCP--MCRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCC--CcCCeee
Confidence 345666666553 222 3344579999999999999987522 22899 5877654
No 52
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.94 E-value=0.015 Score=54.49 Aligned_cols=48 Identities=29% Similarity=0.687 Sum_probs=34.9
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCC
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGL 204 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 204 (334)
...+.|+||++-+.. ......|.|.||.+|+..-+.. + .=.|| .|...
T Consensus 41 ~~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~----g--n~ecp--tcRk~ 88 (381)
T KOG0311|consen 41 DIQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRS----G--NNECP--TCRKK 88 (381)
T ss_pred hhhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHh----c--CCCCc--hHHhh
Confidence 457899999998763 3445689999999999766643 2 22688 57653
No 53
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.83 E-value=0.068 Score=52.06 Aligned_cols=50 Identities=24% Similarity=0.727 Sum_probs=36.5
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
......|++|...+. +++....|||.||..|+..+... ...|| .|...+.
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~-------~~~cp--~~~~~~~ 67 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN-------HQKCP--VCRQELT 67 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc-------CcCCc--ccccccc
Confidence 466799999998765 44443489999999999998865 34677 4544433
No 54
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.68 E-value=0.073 Score=54.15 Aligned_cols=48 Identities=19% Similarity=0.477 Sum_probs=36.2
Q ss_pred ccccccccccccccCCce--eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcC
Q 019929 147 YGPFVCEICAEQKTVHKS--FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDC 201 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C 201 (334)
.....|.||.+....... ...++|+|.|+..|++.|++.+ -.||.+.+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~CR~ 338 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPTCRT 338 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCcchh
Confidence 346889999998764321 4467999999999999999972 37895333
No 55
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.36 E-value=0.093 Score=50.30 Aligned_cols=110 Identities=20% Similarity=0.500 Sum_probs=66.1
Q ss_pred cccccc--ccccc---cCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccC-----C---
Q 019929 149 PFVCEI--CAEQK---TVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDIL-----P--- 215 (334)
Q Consensus 149 ~~~C~I--C~e~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll-----~--- 215 (334)
...||- |.... +...+.....|.-.||..|...|-- +. | |+.... +.++-++ +
T Consensus 273 v~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG------~s----~---Ck~~~~-~~~~l~~~~~~~d~a~ 338 (445)
T KOG1814|consen 273 VVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG------VS----P---CKVKAE-KLIELYLEYLEADEAR 338 (445)
T ss_pred cccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC------CC----c---ccCchH-HHHHHHHHHhhcCHHH
Confidence 466766 43331 1223344457889999999988863 11 2 655533 2222111 1
Q ss_pred -hHHHHHHHHHHHHhhc----C----CCCcccCCCCCCCceEEcCCccccccccCCccccccccccCccC
Q 019929 216 -QDVFDRWGAALCEAVI----P----GAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPW 276 (334)
Q Consensus 216 -~~~~~~y~~~~~~~~~----~----~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 276 (334)
.++-.||.+...+..+ . ..+...|| .|..++....+ .+.+.|..|++.||+.|....
T Consensus 339 k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG--CnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 339 KRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG--CNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC--ccceeeccccccceeehhhhc
Confidence 1345566643333221 1 23456899 99988887643 567999999999999998754
No 56
>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=92.27 E-value=0.069 Score=43.57 Aligned_cols=37 Identities=16% Similarity=0.445 Sum_probs=28.5
Q ss_pred cccccccccccccCCceeEecCCC------CcccHHHHHHHHH
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCS------HAYCTDCMVKYVA 184 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~------H~fC~~Cl~~~~~ 184 (334)
...+|.||++.+...+.+...+|+ |.||.+|++.|-.
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 368999999998763444444776 7799999999943
No 57
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.16 E-value=0.05 Score=47.00 Aligned_cols=33 Identities=27% Similarity=0.871 Sum_probs=26.0
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHH
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVA 184 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 184 (334)
.|.|.||-.++. .++. ..|||.||..|...-+.
T Consensus 196 PF~C~iCKkdy~--spvv-t~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 196 PFLCGICKKDYE--SPVV-TECGHSFCSLCAIRKYQ 228 (259)
T ss_pred ceeehhchhhcc--chhh-hhcchhHHHHHHHHHhc
Confidence 689999999886 3343 48999999999866543
No 58
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.09 E-value=0.063 Score=48.01 Aligned_cols=50 Identities=20% Similarity=0.552 Sum_probs=36.1
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
...|..|+---+ ...|.+..|+|.||..|...-.. -.|| .|+..+....+
T Consensus 3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~---------~~C~--lCkk~ir~i~l 52 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSP---------DVCP--LCKKSIRIIQL 52 (233)
T ss_pred eEEeccccccCC-CCceeeeechhhhhhhhcccCCc---------cccc--cccceeeeeec
Confidence 357998887554 56777889999999999865332 1799 69877655433
No 59
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=92.07 E-value=0.12 Score=49.68 Aligned_cols=35 Identities=20% Similarity=0.532 Sum_probs=27.6
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVA 184 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 184 (334)
++++-|+||..-|. +++. ++|+|..|+.|.+....
T Consensus 2 eeelkc~vc~~f~~--epii-l~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYR--EPII-LPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhcc--CceE-eecccHHHHHHHHhhcc
Confidence 35688999998776 5554 59999999999987554
No 60
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=91.62 E-value=0.065 Score=51.05 Aligned_cols=46 Identities=33% Similarity=0.861 Sum_probs=34.3
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCC
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCR 202 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 202 (334)
...|.||.+.- .-+.+.+|||..|..|+..|-.. ++ .-.||++.|.
T Consensus 369 FeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~s---d~--gq~CPFCRcE 414 (563)
T KOG1785|consen 369 FELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDS---DE--GQTCPFCRCE 414 (563)
T ss_pred HHHHHHhhccC---CCcccccccchHHHHHHHhhccc---CC--CCCCCceeeE
Confidence 45699999853 33667899999999999998643 21 2379987775
No 61
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.51 E-value=0.21 Score=47.21 Aligned_cols=50 Identities=26% Similarity=0.608 Sum_probs=36.5
Q ss_pred CccccccccccccccCCceeEecCCCCc-ccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCch
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHA-YCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEP 207 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 207 (334)
.....+|.||+.+.. +.. +++|.|. .|..|.+..-- ..+ .|| -|.+.+..
T Consensus 287 ~~~gkeCVIClse~r--dt~-vLPCRHLCLCs~Ca~~Lr~---q~n----~CP--ICRqpi~~ 337 (349)
T KOG4265|consen 287 SESGKECVICLSESR--DTV-VLPCRHLCLCSGCAKSLRY---QTN----NCP--ICRQPIEE 337 (349)
T ss_pred ccCCCeeEEEecCCc--ceE-EecchhhehhHhHHHHHHH---hhc----CCC--ccccchHh
Confidence 355789999998744 544 5699999 99999987652 122 799 58876543
No 62
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.45 E-value=0.088 Score=48.47 Aligned_cols=53 Identities=19% Similarity=0.333 Sum_probs=38.6
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
.-+|.||+..-. -+ ..+.|+|.||..|++.-+... ...|+ -|..+|+...+..
T Consensus 7 ~~eC~IC~nt~n--~P-v~l~C~HkFCyiCiKGsy~nd------k~~Ca--vCR~pids~i~~~ 59 (324)
T KOG0824|consen 7 KKECLICYNTGN--CP-VNLYCFHKFCYICIKGSYKND------KKTCA--VCRFPIDSTIDFE 59 (324)
T ss_pred CCcceeeeccCC--cC-ccccccchhhhhhhcchhhcC------CCCCc--eecCCCCcchhcc
Confidence 568999998643 33 356999999999999766532 33598 5998888765443
No 63
>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=90.91 E-value=0.12 Score=46.60 Aligned_cols=75 Identities=20% Similarity=0.428 Sum_probs=40.7
Q ss_pred ccccccccccccccCCceeEecCCCCc-ccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHA-YCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAA 225 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~ 225 (334)
....+|.+|...+..... .=+|. -|..|-+.--...---|...++|| |+-.|--
T Consensus 63 ~p~v~CrVCq~~I~i~gk----~~QhVVkC~~CnEATPIr~aPpGKKYVRCP---CNCLLIC------------------ 117 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGK----MHQHVVKCSVCNEATPIRNAPPGKKYVRCP---CNCLLIC------------------ 117 (256)
T ss_pred CceEEeecCCceecccCc----cceeeEECCCCCccccccCCCCCCeeEecC---CceEEEe------------------
Confidence 357899999876543221 11222 344444322211112255667777 4332211
Q ss_pred HHHhhcCCCCcccCCCCCCCceEEcC
Q 019929 226 LCEAVIPGAQKFYCPFKDCSAMLIDD 251 (334)
Q Consensus 226 ~~~~~~~~~~~~~CP~p~C~~~~~~~ 251 (334)
...+..+.||.|+|..++-..
T Consensus 118 -----k~sS~rIaCPRp~CkRiI~L~ 138 (256)
T PF09788_consen 118 -----KSSSQRIACPRPNCKRIINLG 138 (256)
T ss_pred -----ecccccccCCCCCCcceEEeC
Confidence 125667899999999887654
No 64
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.66 E-value=0.16 Score=34.26 Aligned_cols=25 Identities=28% Similarity=0.588 Sum_probs=19.0
Q ss_pred cccCCCCceeeecc--CCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKD--GCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~--GCnhMtC~-Cg~ 334 (334)
+.||.|+.++...+ +-+++.|+ |||
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCC
Confidence 46999999877644 35689996 997
No 65
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.49 E-value=0.31 Score=46.64 Aligned_cols=60 Identities=17% Similarity=0.347 Sum_probs=45.9
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
...|.|||=-+.-+..++...+.|||.++++=+..... +|...++|| -|+........++
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence 45799999887776666666779999999987766654 455689999 6988777665554
No 66
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.48 E-value=0.18 Score=31.69 Aligned_cols=30 Identities=23% Similarity=0.710 Sum_probs=22.4
Q ss_pred ccCCCCCCCceEEcCCc---cccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGE---EVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~---~~~~~~~C~~C~~~f 268 (334)
+.|| .|+..+..++. .....++|+.|++.|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 5788 99988776643 345579999999876
No 67
>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=90.46 E-value=0.36 Score=32.43 Aligned_cols=42 Identities=14% Similarity=0.543 Sum_probs=29.7
Q ss_pred ccccccccccCCceeEecCCC-----CcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 151 VCEICAEQKTVHKSFHIKGCS-----HAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
.|-||++.....+.+. .+|. |.+...|+..|+..+- ...||.
T Consensus 1 ~CrIC~~~~~~~~~l~-~PC~C~G~~~~vH~~Cl~~W~~~~~-----~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLV-SPCRCKGSLKYVHQECLERWINESG-----NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeE-eccccCCchhHHHHHHHHHHHHHcC-----CCcCCC
Confidence 3889998444445454 4785 8899999999997653 237873
No 68
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.05 E-value=0.27 Score=47.75 Aligned_cols=49 Identities=24% Similarity=0.680 Sum_probs=36.1
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCch
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEP 207 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 207 (334)
..+|+|.||+..+. .++.. +|||.||..|+..-.. ..-.|| .|...+..
T Consensus 82 ~sef~c~vc~~~l~--~pv~t-pcghs~c~~Cl~r~ld-------~~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY--PPVVT-PCGHSFCLECLDRSLD-------QETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC--CCccc-cccccccHHHHHHHhc-------cCCCCc--cccccccc
Confidence 56899999998765 44554 9999999999776222 234788 58877764
No 69
>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=89.80 E-value=0.071 Score=47.43 Aligned_cols=51 Identities=20% Similarity=0.584 Sum_probs=36.8
Q ss_pred cccccccccccC-Cce--eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 150 FVCEICAEQKTV-HKS--FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 150 ~~C~IC~e~~~~-~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
--||||-.+.-. .++ +....|-|.+|.+|+...|.. .+-.||..+|+.++.
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~------GpAqCP~~gC~kILR 64 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR------GPAQCPYKGCGKILR 64 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC------CCCCCCCccHHHHHH
Confidence 469999876533 232 222349999999999988864 366899999986544
No 70
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.53 E-value=0.6 Score=42.91 Aligned_cols=69 Identities=14% Similarity=0.393 Sum_probs=50.1
Q ss_pred CccccccccccccccCC-ceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCCh-HHHHHHH
Q 019929 146 VYGPFVCEICAEQKTVH-KSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQ-DVFDRWG 223 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~-~~~~~y~ 223 (334)
....|.|||...++... .++.+.+|||.|+..++...- . .-.|| .|..+|...+|-.|-+. +.++.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~----~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K----SKKCP--VCGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c----ccccc--ccCCccccCCEEEecCCccHHHHHH
Confidence 35689999999988654 455677999999999998872 1 12499 69999998877766553 3444444
Q ss_pred H
Q 019929 224 A 224 (334)
Q Consensus 224 ~ 224 (334)
.
T Consensus 180 ~ 180 (260)
T PF04641_consen 180 E 180 (260)
T ss_pred H
Confidence 3
No 71
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.36 E-value=0.26 Score=47.31 Aligned_cols=53 Identities=26% Similarity=0.615 Sum_probs=38.5
Q ss_pred cccccccccccc--CCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchh
Q 019929 149 PFVCEICAEQKT--VHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 149 ~~~C~IC~e~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 208 (334)
..+|+||++.+. .......+.|||.|=.+|++.|+. + .....|| .|...-...
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k----~~~~~cp--~c~~katkr 58 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-K----KTKMQCP--LCSGKATKR 58 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-h----hhhhhCc--ccCChhHHH
Confidence 468999999764 333344569999999999999993 2 3467899 577654443
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=88.99 E-value=0.37 Score=50.29 Aligned_cols=54 Identities=24% Similarity=0.642 Sum_probs=42.3
Q ss_pred ccccccccccccccCC-ceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCC
Q 019929 147 YGPFVCEICAEQKTVH-KSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCR 202 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 202 (334)
...++|.||++.+... .+++...|-|.|-..|++.|....-.++...-+||. |.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA--CQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc--cc
Confidence 4479999999988654 457777899999999999999985445555668994 55
No 73
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.87 E-value=0.38 Score=45.26 Aligned_cols=37 Identities=22% Similarity=0.533 Sum_probs=27.7
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHh
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAA 185 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 185 (334)
.++.-.|+||+-.- ..- + +.+|+|.-|..|+.+|+..
T Consensus 419 ~sEd~lCpICyA~p-i~A-v-f~PC~H~SC~~CI~qHlmN 455 (489)
T KOG4692|consen 419 DSEDNLCPICYAGP-INA-V-FAPCSHRSCYGCITQHLMN 455 (489)
T ss_pred CcccccCcceeccc-chh-h-ccCCCCchHHHHHHHHHhc
Confidence 35678899999632 122 2 3599999999999999864
No 74
>PHA00626 hypothetical protein
Probab=88.63 E-value=0.31 Score=33.34 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=19.4
Q ss_pred ccCCCCc-eeeeccCCCc----eEee-cCC
Q 019929 311 RCPNCRY-YVEKKDGCMY----MKCR-SVF 334 (334)
Q Consensus 311 ~CP~C~~-~IeK~~GCnh----MtC~-Cg~ 334 (334)
.||+|+. -|.|.+=|+. ..|+ |||
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCC
Confidence 5999999 5889887766 7785 987
No 75
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=88.37 E-value=0.29 Score=33.09 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=18.5
Q ss_pred CccccCCCCc-eeeeccCCCceEe-ecCC
Q 019929 308 KWKRCPNCRY-YVEKKDGCMYMKC-RSVF 334 (334)
Q Consensus 308 ~~k~CP~C~~-~IeK~~GCnhMtC-~Cg~ 334 (334)
..+.||+|+. .+.... +.++| +|||
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCC
Confidence 3479999998 444444 79999 4997
No 76
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.26 E-value=0.51 Score=48.87 Aligned_cols=51 Identities=22% Similarity=0.400 Sum_probs=31.0
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchh
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 208 (334)
.-.|++|+..+.......-..|+|+||..|+..|-.. .-.|| .|...|..-
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~-------aqTCP--iDR~EF~~v 173 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC-------AQTCP--VDRGEFGEV 173 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh-------cccCc--hhhhhhhee
Confidence 3457777766543333333478888888888777654 22677 466655543
No 77
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.21 E-value=0.23 Score=47.27 Aligned_cols=48 Identities=23% Similarity=0.703 Sum_probs=33.4
Q ss_pred ccccccccccccCCcee-EecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCC
Q 019929 149 PFVCEICAEQKTVHKSF-HIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCR 202 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 202 (334)
...|.||-+-++....+ .+-.|||.|...|+.+|++..-.. -.||. |.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~----R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN----RGCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc----CCCCc--ee
Confidence 35799996666654433 343599999999999999864332 36774 55
No 78
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=87.28 E-value=0.48 Score=44.38 Aligned_cols=57 Identities=26% Similarity=0.553 Sum_probs=39.6
Q ss_pred cccccccccccccCCc-eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 148 GPFVCEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
+.-.|++|+++....+ .|.-.+||-.+|+-||.. +...+ .=+|| -|....+.+.++-
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~l-----ngrcp--acrr~y~denv~~ 70 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNL-----NGRCP--ACRRKYDDENVRY 70 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhc-----cCCCh--HhhhhccccceeE
Confidence 3455999999876543 233348999999999964 34333 23899 5998888776653
No 79
>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=87.16 E-value=0.34 Score=27.99 Aligned_cols=23 Identities=35% Similarity=0.910 Sum_probs=16.7
Q ss_pred cCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
.|| .|...+... ...||.||+.|
T Consensus 2 ~CP--~C~~~V~~~------~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPES------AKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchhh------cCcCCCCCCCC
Confidence 577 898776432 26899999876
No 80
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.91 E-value=0.47 Score=29.64 Aligned_cols=30 Identities=30% Similarity=0.700 Sum_probs=21.7
Q ss_pred ccCCCCCCCceEEcCCc---cccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGE---EVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~---~~~~~~~C~~C~~~f 268 (334)
+.|| .|+..+..++. .....++|+.|++.|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 5688 89987766533 334569999998875
No 81
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.89 E-value=0.22 Score=45.20 Aligned_cols=56 Identities=20% Similarity=0.474 Sum_probs=40.8
Q ss_pred cccccccccccccCCc-------eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 148 GPFVCEICAEQKTVHK-------SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
+.-.|.||-..+..+. ....++|+|.|...|++.|... |. .-.|| -|+..++...+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK-kqtCP--YCKekVdl~rm 285 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK-KQTCP--YCKEKVDLKRM 285 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC-CCCCc--hHHHHhhHhhh
Confidence 4567999988765433 3334699999999999999865 22 23799 69988876543
No 82
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=85.72 E-value=2.5 Score=32.72 Aligned_cols=33 Identities=18% Similarity=0.455 Sum_probs=26.7
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMV 180 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~ 180 (334)
.+...|++|...+.. ..|...+|||.|...|++
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 456779999998866 556667999999999975
No 83
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=85.43 E-value=3.9 Score=38.41 Aligned_cols=48 Identities=21% Similarity=0.513 Sum_probs=34.5
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCC
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGL 204 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 204 (334)
....|+||...... ...+..=|-.||-.|+.+|+.. . =+||..+|+..
T Consensus 299 ~~~~CpvClk~r~N--ptvl~vSGyVfCY~Ci~~Yv~~---~----~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKRQN--PTVLEVSGYVFCYPCIFSYVVN---Y----GHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhccCC--CceEEecceEEeHHHHHHHHHh---c----CCCCccCCcch
Confidence 46789999976543 2233345899999999999973 2 27998777654
No 84
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.15 E-value=0.8 Score=41.14 Aligned_cols=57 Identities=12% Similarity=0.225 Sum_probs=43.7
Q ss_pred ccccccccccccccCCc-eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 147 YGPFVCEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
+..+.|+||-+.+...- ...+.+|||.||.+|...++.. ...|| -|..++...+|-.
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-------D~v~p--v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-------DMVDP--VTDKPLKDRDIIG 276 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-------ccccc--CCCCcCcccceEe
Confidence 35789999999887543 3457799999999999998863 45678 5888877766544
No 85
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=84.97 E-value=0.63 Score=42.96 Aligned_cols=42 Identities=21% Similarity=0.429 Sum_probs=34.7
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhh
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKL 187 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 187 (334)
..+...|.||+--|..++.|...+|.|+|..-||..|+..-.
T Consensus 112 n~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 112 NHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 345678999998887777787789999999999999986544
No 86
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=84.69 E-value=0.67 Score=31.11 Aligned_cols=28 Identities=29% Similarity=0.697 Sum_probs=19.2
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+|| .|+..+..........+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 788 9999877654433335778888753
No 87
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.68 E-value=1.9 Score=45.54 Aligned_cols=41 Identities=22% Similarity=0.579 Sum_probs=33.0
Q ss_pred CCccccccccccccccCCceeEecCCCCcccHHHHHHHHHhh
Q 019929 145 IVYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAK 186 (334)
Q Consensus 145 ~~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~ 186 (334)
...+.-.|.+|.-.+-. ++|.+.+|||.|.++|+..++..-
T Consensus 813 v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 813 VLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred EecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHHcc
Confidence 35667899999987755 456667999999999999988654
No 88
>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=84.50 E-value=0.45 Score=29.57 Aligned_cols=28 Identities=21% Similarity=0.678 Sum_probs=18.6
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.+|| .|+.++.+........ .|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 5899 9999988765443333 68877764
No 89
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.44 E-value=1.5 Score=40.55 Aligned_cols=45 Identities=20% Similarity=0.753 Sum_probs=33.3
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
.+-|+.|-.... +......|+|.||.+|+..-+.. ..+.|| .|..
T Consensus 274 ~LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d------sDf~Cp--nC~r 318 (427)
T COG5222 274 SLKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD------SDFKCP--NCSR 318 (427)
T ss_pred cccCcchhhhhh--CcccCccccchHHHHHHhhhhhh------ccccCC--Cccc
Confidence 488999987654 44445689999999999876643 367999 4654
No 90
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=83.59 E-value=1.4 Score=40.65 Aligned_cols=52 Identities=21% Similarity=0.628 Sum_probs=35.3
Q ss_pred cccccccccc-CCce-eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhh
Q 019929 151 VCEICAEQKT-VHKS-FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYC 210 (334)
Q Consensus 151 ~C~IC~e~~~-~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 210 (334)
.|++|-.+.- ..++ +..-+|+|..|.+|+-..+.. | +-.|| +|..++-..-+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g--~~~Cp--eC~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G--PAQCP--ECMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C--CCCCC--cccchhhhccc
Confidence 4888876542 2232 223489999999999988864 2 44799 89987766543
No 91
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.46 E-value=1.1 Score=44.48 Aligned_cols=45 Identities=29% Similarity=0.758 Sum_probs=30.4
Q ss_pred cccCCCCCCCceEEcCCccccccccCCc--cccccccccCccC--CC---CCCchh
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPN--CRRLFCAQCQVPW--HS---GINCVE 284 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~--C~~~fC~~C~~~~--H~---~~tC~~ 284 (334)
...|| .|...+..+.+ .+...|.. |++.||+.|...| |. +..|..
T Consensus 226 tk~CP--~c~~~iek~~g--c~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~ 277 (444)
T KOG1815|consen 226 TKECP--KCKVPIEKDGG--CNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNR 277 (444)
T ss_pred CccCC--CcccchhccCC--ccccccccCCcCCeeceeeecccccccccceeeeee
Confidence 34588 89887776543 33356655 9999999997776 64 345643
No 92
>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=83.45 E-value=1.2 Score=26.85 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=17.3
Q ss_pred CccccCCCCceeeeccCCCceEee-cCC
Q 019929 308 KWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 308 ~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
+.+.||+|+.+.+...|=.-|.|. ||+
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcC
Confidence 347899999999998887888895 874
No 93
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.10 E-value=1.1 Score=29.44 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=14.1
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|+..++-..+=..++|+ ||+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCC
Confidence 3577777766554333356664 663
No 94
>PHA03096 p28-like protein; Provisional
Probab=83.09 E-value=0.66 Score=43.13 Aligned_cols=39 Identities=21% Similarity=0.473 Sum_probs=30.1
Q ss_pred cccccccccccC----Ccee-EecCCCCcccHHHHHHHHHhhhh
Q 019929 150 FVCEICAEQKTV----HKSF-HIKGCSHAYCTDCMVKYVAAKLE 188 (334)
Q Consensus 150 ~~C~IC~e~~~~----~~~~-~~~~C~H~fC~~Cl~~~~~~~i~ 188 (334)
..|.||++.... ...| .+..|.|.||..|.+.|......
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 789999987642 2233 34589999999999999988763
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.76 E-value=0.98 Score=49.44 Aligned_cols=29 Identities=31% Similarity=0.899 Sum_probs=19.6
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccc-----ccccCcc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLF-----CAQCQVP 275 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f-----C~~C~~~ 275 (334)
+.|| .|+.... ..+|+.||... |..|+..
T Consensus 668 rkCP--kCG~~t~--------~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCP--SCGTETY--------ENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECC--CCCCccc--------cccCcccCCcCCCceeCccCCCc
Confidence 5788 8886432 14788888664 7777764
No 96
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=82.72 E-value=0.75 Score=30.68 Aligned_cols=26 Identities=23% Similarity=0.345 Sum_probs=17.1
Q ss_pred ccccCCCCceeeeccCCCceEe-ecCC
Q 019929 309 WKRCPNCRYYVEKKDGCMYMKC-RSVF 334 (334)
Q Consensus 309 ~k~CP~C~~~IeK~~GCnhMtC-~Cg~ 334 (334)
-+.||+|+--+.-..-=+...| +|||
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 3799999964433332336778 6887
No 97
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=82.34 E-value=0.8 Score=28.27 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=13.5
Q ss_pred cccCCCCceeeec----cCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKK----DGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~----~GCnhMtC~-Cg~ 334 (334)
|.||.|+.+++.. ++=..+.|. |||
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 5799999988862 556677785 885
No 98
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=81.35 E-value=0.77 Score=48.55 Aligned_cols=23 Identities=30% Similarity=0.986 Sum_probs=20.9
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
..||.|+..+...+||. +|+ |||
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~ 748 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGY 748 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCC
Confidence 36999999999999998 996 998
No 99
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=81.20 E-value=1.1 Score=43.73 Aligned_cols=39 Identities=18% Similarity=0.479 Sum_probs=29.8
Q ss_pred CccccccccccccccCCc-eeEecCCCCcccHHHHHHHHH
Q 019929 146 VYGPFVCEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVA 184 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~ 184 (334)
..+.-+|+||++....+- .+....|.|.|--.|+..|+.
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~ 211 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD 211 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc
Confidence 456789999999775432 233347999999999999874
No 100
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=80.86 E-value=0.55 Score=48.88 Aligned_cols=52 Identities=29% Similarity=0.779 Sum_probs=37.2
Q ss_pred cccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
++|.||.+ ....+ +..|+|.||.+||..++...-. ..|| .|...+....+..
T Consensus 455 ~~c~ic~~---~~~~~-it~c~h~~c~~c~~~~i~~~~~-----~~~~--~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD---LDSFF-ITRCGHDFCVECLKKSIQQSEN-----APCP--LCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc---cccce-eecccchHHHHHHHhccccccC-----CCCc--HHHHHHHHHHHhh
Confidence 89999998 33444 4489999999999999865321 2677 6887766654443
No 101
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.84 E-value=0.5 Score=32.25 Aligned_cols=45 Identities=31% Similarity=0.650 Sum_probs=31.6
Q ss_pred cccccccccccCCceeEecCCCCc-ccHHHHHHHHHhhhhCCeeeeecCCCcCCCCC
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHA-YCTDCMVKYVAAKLEENITAIRCPVVDCRGLL 205 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 205 (334)
-+|.||++.-- +.+ +-.|||. +|-+|-...+.. ..-.|| -|..++
T Consensus 8 dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~~------~~g~CP--iCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKKA------LHGCCP--ICRAPI 53 (62)
T ss_pred cceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHHc------cCCcCc--chhhHH
Confidence 68999998532 222 3479998 999999888764 123688 577654
No 102
>PRK04023 DNA polymerase II large subunit; Validated
Probab=79.62 E-value=1.3 Score=47.32 Aligned_cols=32 Identities=25% Similarity=0.702 Sum_probs=21.7
Q ss_pred cccCCCCCCCceEEcCCccccccccCCcccc-----ccccccCccCC
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRR-----LFCAQCQVPWH 277 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~-----~fC~~C~~~~H 277 (334)
.++|| .|+... ....||.||. .||..|+....
T Consensus 626 ~RfCp--sCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 626 RRKCP--SCGKET--------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred CccCC--CCCCcC--------CcccCCCCCCCCCcceeCccccCcCC
Confidence 45888 888652 2378888885 47888866433
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=79.48 E-value=1.1 Score=28.03 Aligned_cols=30 Identities=17% Similarity=0.507 Sum_probs=20.0
Q ss_pred ccCCCCCCCceEEcCCc---cccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGE---EVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~---~~~~~~~C~~C~~~f 268 (334)
+.|| .|+..+..+.. .....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688 89987666532 122358999998765
No 104
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=79.03 E-value=0.75 Score=31.54 Aligned_cols=47 Identities=26% Similarity=0.483 Sum_probs=30.6
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhh
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEY 209 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 209 (334)
...|-.|...-. . -.+++|+|.+|..||-..- .=.||. |...+....
T Consensus 7 ~~~~~~~~~~~~--~-~~~~pCgH~I~~~~f~~~r---------YngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFVGT--K-GTVLPCGHLICDNCFPGER---------YNGCPF--CGTPFEFDD 53 (55)
T ss_pred ceeEEEcccccc--c-cccccccceeeccccChhh---------ccCCCC--CCCcccCCC
Confidence 455666654322 2 2356999999999996432 227994 888877654
No 105
>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=79.00 E-value=6.2 Score=31.55 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=22.5
Q ss_pred cccccccccccccC--CceeEecCCCCcccHHHHHH
Q 019929 148 GPFVCEICAEQKTV--HKSFHIKGCSHAYCTDCMVK 181 (334)
Q Consensus 148 ~~~~C~IC~e~~~~--~~~~~~~~C~H~fC~~Cl~~ 181 (334)
....|.+|...|.. +.......|+|.+|..|-..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 45689999887632 22344568999999998654
No 106
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.16 E-value=2.4 Score=45.06 Aligned_cols=53 Identities=26% Similarity=0.555 Sum_probs=37.2
Q ss_pred ccccccccccccccCCc-e---eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 147 YGPFVCEICAEQKTVHK-S---FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~-~---~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
+...+|+||+......+ . -....|.|.|...|+-.|+.+.-+ -.|| -|...++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~-----s~CP--lCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSAR-----SNCP--LCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCC-----CCCC--ccccccc
Confidence 34678999998664111 1 123479999999999999987532 3799 5876665
No 107
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.27 E-value=0.74 Score=42.43 Aligned_cols=46 Identities=26% Similarity=0.609 Sum_probs=33.3
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
.|-|.||-..|. +++. ..|+|+||..|....+.. .-.|+ -|...+.
T Consensus 241 Pf~c~icr~~f~--~pVv-t~c~h~fc~~ca~~~~qk-------~~~c~--vC~~~t~ 286 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVV-TKCGHYFCEVCALKPYQK-------GEKCY--VCSQQTH 286 (313)
T ss_pred Cccccccccccc--cchh-hcCCceeehhhhcccccc-------CCcce--ecccccc
Confidence 578999999876 4444 489999999999877753 23566 4766443
No 108
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.65 E-value=1.4 Score=45.62 Aligned_cols=14 Identities=29% Similarity=0.530 Sum_probs=8.8
Q ss_pred CCccccCCCCceee
Q 019929 307 EKWKRCPNCRYYVE 320 (334)
Q Consensus 307 ~~~k~CP~C~~~Ie 320 (334)
.+.+.||+|+...-
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 44567777776543
No 109
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.93 E-value=1.4 Score=30.62 Aligned_cols=25 Identities=28% Similarity=0.680 Sum_probs=16.7
Q ss_pred cccCCCC-ceeeeccCC----CceEe-ecCC
Q 019929 310 KRCPNCR-YYVEKKDGC----MYMKC-RSVF 334 (334)
Q Consensus 310 k~CP~C~-~~IeK~~GC----nhMtC-~Cg~ 334 (334)
-.||+|+ ..|-+-.-| |--+| .|||
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 5788888 677665555 44567 4776
No 110
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.19 E-value=2.9 Score=29.13 Aligned_cols=26 Identities=23% Similarity=0.597 Sum_probs=15.6
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.|. .|+..+.... ....+.||.||..
T Consensus 9 ~Ct--SCg~~i~~~~--~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCT--SCGIEIAPRE--KAVKFLCPNCGEV 34 (59)
T ss_pred ccc--CCCCcccCCC--ccCEeeCCCCCCe
Confidence 455 6776554332 2345788888865
No 111
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.64 E-value=5.9 Score=37.45 Aligned_cols=69 Identities=29% Similarity=0.448 Sum_probs=41.5
Q ss_pred CCccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHH
Q 019929 145 IVYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWG 223 (334)
Q Consensus 145 ~~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~ 223 (334)
..+++..|.||.+... -..+++|+|.+|.-|....-..- ..-.|| -|......-.+-.-.+.++-++|.
T Consensus 57 tDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY-----~~K~C~--~CrTE~e~V~fT~~~~~DI~D~~~ 125 (493)
T COG5236 57 TDEENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALY-----MQKGCP--LCRTETEAVVFTASSPADITDRRQ 125 (493)
T ss_pred cccccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHH-----hccCCC--ccccccceEEEecCCCCcchhHhh
Confidence 3567899999998654 23467999999999976543221 123688 477654443333333334444443
No 112
>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=73.30 E-value=2.7 Score=39.43 Aligned_cols=53 Identities=21% Similarity=0.477 Sum_probs=31.3
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRY 317 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~ 317 (334)
-|| -|..-....+.-.. .+. .||+.||..|... . . ..+..+||.|+.
T Consensus 5 ~CP--~Ck~~~y~np~~kl-~i~--~CGH~~C~sCv~~-----------------------l----~-~~~~~~CP~C~~ 51 (309)
T TIGR00570 5 GCP--RCKTTKYRNPSLKL-MVN--VCGHTLCESCVDL-----------------------L----F-VRGSGSCPECDT 51 (309)
T ss_pred CCC--cCCCCCccCccccc-ccC--CCCCcccHHHHHH-----------------------H----h-cCCCCCCCCCCC
Confidence 588 77764333322111 122 5999999988431 0 1 233458999998
Q ss_pred eeeecc
Q 019929 318 YVEKKD 323 (334)
Q Consensus 318 ~IeK~~ 323 (334)
.+-|+.
T Consensus 52 ~lrk~~ 57 (309)
T TIGR00570 52 PLRKNN 57 (309)
T ss_pred ccchhh
Confidence 887753
No 113
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.59 E-value=7.2 Score=41.07 Aligned_cols=11 Identities=27% Similarity=0.609 Sum_probs=8.4
Q ss_pred CccccCCCCce
Q 019929 308 KWKRCPNCRYY 318 (334)
Q Consensus 308 ~~k~CP~C~~~ 318 (334)
....||+|+..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 34789999876
No 114
>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=72.49 E-value=2.5 Score=28.07 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=20.0
Q ss_pred CccccC--CCCceeeeccCCCceEe-ecCC
Q 019929 308 KWKRCP--NCRYYVEKKDGCMYMKC-RSVF 334 (334)
Q Consensus 308 ~~k~CP--~C~~~IeK~~GCnhMtC-~Cg~ 334 (334)
.-+.|| .|+.-|.-..--+..+| +|||
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 348999 99997776666788999 6986
No 115
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=72.35 E-value=2.2 Score=34.76 Aligned_cols=25 Identities=32% Similarity=0.623 Sum_probs=20.1
Q ss_pred CccccCCCCceeeeccCCCceEee-cCC
Q 019929 308 KWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 308 ~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
..+.||.|+.+..+..| -+.|+ |||
T Consensus 27 L~~hCp~Cg~PLF~KdG--~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGTPLFRKDG--EVFCPVCGY 52 (131)
T ss_pred HHhhCcccCCcceeeCC--eEECCCCCc
Confidence 34899999998888776 68885 885
No 116
>PLN03086 PRLI-interacting factor K; Provisional
Probab=72.08 E-value=9.6 Score=38.88 Aligned_cols=97 Identities=20% Similarity=0.494 Sum_probs=0.0
Q ss_pred eeecCCCcCCCCCchhhhhccCChHHHHHHHHHHHHhhcCCCCcccCCCCCCCceEEcCCccccccccCCcccccc----
Q 019929 193 AIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAALCEAVIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLF---- 268 (334)
Q Consensus 193 ~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f---- 268 (334)
.+.|| .|...++...+... ...=.-..+.||+.+|+..+.......- +.|+.|+..|
T Consensus 407 ~V~C~--NC~~~i~l~~l~lH---------------e~~C~r~~V~Cp~~~Cg~v~~r~el~~H--~~C~~Cgk~f~~s~ 467 (567)
T PLN03086 407 TVECR--NCKHYIPSRSIALH---------------EAYCSRHNVVCPHDGCGIVLRVEEAKNH--VHCEKCGQAFQQGE 467 (567)
T ss_pred eEECC--CCCCccchhHHHHH---------------HhhCCCcceeCCcccccceeeccccccC--ccCCCCCCccchHH
Q ss_pred -------------ccccCccC-------CCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeecc-----
Q 019929 269 -------------CAQCQVPW-------HSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKKD----- 323 (334)
Q Consensus 269 -------------C~~C~~~~-------H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~~----- 323 (334)
|. |+... |....|. .....|+.|+..+ ..|
T Consensus 468 LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp-----------------------~Kpi~C~fC~~~v-~~g~~~~d 522 (567)
T PLN03086 468 MEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCP-----------------------LRLITCRFCGDMV-QAGGSAMD 522 (567)
T ss_pred HHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCC-----------------------CCceeCCCCCCcc-ccCccccc
Q ss_pred ---------------CCCceEee-cC
Q 019929 324 ---------------GCMYMKCR-SV 333 (334)
Q Consensus 324 ---------------GCnhMtC~-Cg 333 (334)
|-.|..|. ||
T Consensus 523 ~~d~~s~Lt~HE~~CG~rt~~C~~Cg 548 (567)
T PLN03086 523 VRDRLRGMSEHESICGSRTAPCDSCG 548 (567)
T ss_pred hhhhhhhHHHHHHhcCCcceEccccC
No 117
>PRK00420 hypothetical protein; Validated
Probab=72.03 E-value=2.4 Score=33.69 Aligned_cols=24 Identities=33% Similarity=0.564 Sum_probs=19.9
Q ss_pred CccccCCCCceeee-ccCCCceEee-cC
Q 019929 308 KWKRCPNCRYYVEK-KDGCMYMKCR-SV 333 (334)
Q Consensus 308 ~~k~CP~C~~~IeK-~~GCnhMtC~-Cg 333 (334)
....||.|+.++.+ .+| +..|+ ||
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg 47 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHG 47 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCC
Confidence 44899999999998 666 78885 87
No 118
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.57 E-value=1.3 Score=39.45 Aligned_cols=37 Identities=30% Similarity=0.682 Sum_probs=25.2
Q ss_pred ccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeee
Q 019929 257 QESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 257 ~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
+.++| ||+.|||-|...| . ....+.+.||-|+..|..
T Consensus 60 PVvTl--CGHLFCWpClyqW------------l--------------~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 60 PVVTL--CGHLFCWPCLYQW------------L--------------QTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CEEee--cccceehHHHHHH------------H--------------hhcCCCeeCCcccccccc
Confidence 34666 9999999996533 1 113556888988876653
No 119
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=71.29 E-value=2.9 Score=27.80 Aligned_cols=26 Identities=19% Similarity=0.526 Sum_probs=19.1
Q ss_pred ccccCCCCceeeeccC--------CCceEeecCC
Q 019929 309 WKRCPNCRYYVEKKDG--------CMYMKCRSVF 334 (334)
Q Consensus 309 ~k~CP~C~~~IeK~~G--------CnhMtC~Cg~ 334 (334)
.-.||+|+.-..-+++ =-+=||+|||
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGf 46 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGF 46 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeecccc
Confidence 5799999986655543 4456799987
No 120
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=70.79 E-value=2.6 Score=39.45 Aligned_cols=47 Identities=23% Similarity=0.560 Sum_probs=34.2
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
....++||||++.+...- ++. .=||..|.+|-.. ..-+||. |...++
T Consensus 45 ~~~lleCPvC~~~l~~Pi-~QC-~nGHlaCssC~~~----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPI-FQC-DNGHLACSSCRTK----------VSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCcccc-eec-CCCcEehhhhhhh----------hcccCCc--cccccc
Confidence 456799999999876432 332 4589999999862 2348994 988887
No 121
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=70.69 E-value=1 Score=46.57 Aligned_cols=30 Identities=23% Similarity=0.801 Sum_probs=21.7
Q ss_pred CccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCcee
Q 019929 262 PNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYV 319 (334)
Q Consensus 262 ~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~I 319 (334)
++|++.||..|-.+ . + ....++||+|+..+
T Consensus 659 ~kC~H~FC~~Cvq~------------r---------------~-etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 659 TKCGHVFCEECVQT------------R---------------Y-ETRQRKCPKCNAAF 688 (698)
T ss_pred HhcchHHHHHHHHH------------H---------------H-HHhcCCCCCCCCCC
Confidence 47999999999541 0 1 24458999999865
No 122
>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=70.59 E-value=3.7 Score=28.62 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=19.4
Q ss_pred cccCCCCc----eeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRY----YVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~----~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|+. ..-+..|=.++.|. |||
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~ 39 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGY 39 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCC
Confidence 47999987 34457777999995 998
No 123
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.39 E-value=1.1 Score=38.24 Aligned_cols=31 Identities=29% Similarity=0.857 Sum_probs=22.2
Q ss_pred CccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeee
Q 019929 262 PNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 262 ~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
.+||++||..|.+ ++ ..++..||-|+..|.+
T Consensus 149 TkCGHvFC~~Cik---------------------------~a--lk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 149 TKCGHVFCSQCIK---------------------------DA--LKNTNKCPTCRKKITH 179 (187)
T ss_pred cccchhHHHHHHH---------------------------HH--HHhCCCCCCcccccch
Confidence 4799999998843 11 2355899999976654
No 124
>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=70.33 E-value=2.9 Score=29.82 Aligned_cols=27 Identities=22% Similarity=0.498 Sum_probs=22.0
Q ss_pred CccccCCCCceeeeccCCCceEee-cCC
Q 019929 308 KWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 308 ~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
..+.||.|+....+...=..++|+ |||
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCC
Confidence 558999999999985555678896 986
No 125
>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=69.29 E-value=4 Score=26.29 Aligned_cols=23 Identities=30% Similarity=0.653 Sum_probs=18.1
Q ss_pred ccccCCCCceeee-ccCCCceEee-cC
Q 019929 309 WKRCPNCRYYVEK-KDGCMYMKCR-SV 333 (334)
Q Consensus 309 ~k~CP~C~~~IeK-~~GCnhMtC~-Cg 333 (334)
...||.|+.++.+ .+| .+.|. |+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3799999998888 666 67784 75
No 126
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=69.20 E-value=0.96 Score=42.26 Aligned_cols=83 Identities=20% Similarity=0.515 Sum_probs=44.8
Q ss_pred CcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHHH-HHhhcC-----CCCcccCCCCCCC
Q 019929 172 HAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAAL-CEAVIP-----GAQKFYCPFKDCS 245 (334)
Q Consensus 172 H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~~-~~~~~~-----~~~~~~CP~p~C~ 245 (334)
-+||..|-..+.. .++.|| .|...+ ++++.+...|..++ +..+.+ ..+..+|- .|+
T Consensus 276 Gy~CP~CkakvCs-------LP~eCp--iC~ltL-------Vss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~ 337 (378)
T KOG2807|consen 276 GYFCPQCKAKVCS-------LPIECP--ICSLTL-------VSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQ 337 (378)
T ss_pred ceeCCcccCeeec-------CCccCC--ccceeE-------ecchHHHHHHHhhcCCcchhhccccccCCCccee--eec
Confidence 4566666555543 477777 465432 23345555555443 111111 12223566 663
Q ss_pred ceEEcCCccccccccCCccccccccccCccCC
Q 019929 246 AMLIDDGEEVIQESECPNCRRLFCAQCQVPWH 277 (334)
Q Consensus 246 ~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 277 (334)
.- .......+|+.|+..||..|..-.|
T Consensus 338 ~~-----~~~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 338 GE-----LLSSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred cc-----cCCCCcEEchhccceeeccchHHHH
Confidence 32 2223458999999999998865333
No 127
>PF12773 DZR: Double zinc ribbon
Probab=68.54 E-value=3.9 Score=27.10 Aligned_cols=10 Identities=50% Similarity=1.002 Sum_probs=5.9
Q ss_pred CCccccCCCC
Q 019929 307 EKWKRCPNCR 316 (334)
Q Consensus 307 ~~~k~CP~C~ 316 (334)
.+++.||+|+
T Consensus 41 ~~~~fC~~CG 50 (50)
T PF12773_consen 41 PNAKFCPNCG 50 (50)
T ss_pred CCcCccCccc
Confidence 4456666664
No 128
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=68.51 E-value=4.8 Score=26.39 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=20.2
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
+.|| +|+..+..+.... .+.||.||..+
T Consensus 4 y~C~--~CG~~~~~~~~~~--~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCA--RCGREVELDEYGT--GVRCPYCGYRI 31 (46)
T ss_pred EECC--CCCCEEEECCCCC--ceECCCCCCeE
Confidence 4688 8998877664432 58999998754
No 129
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.03 E-value=9.1 Score=40.04 Aligned_cols=23 Identities=30% Similarity=0.765 Sum_probs=15.0
Q ss_pred cccccCCcccccc-ccccCcc--CCC
Q 019929 256 IQESECPNCRRLF-CAQCQVP--WHS 278 (334)
Q Consensus 256 ~~~~~C~~C~~~f-C~~C~~~--~H~ 278 (334)
.+.+.|..||+.+ |.+|..+ +|.
T Consensus 381 ap~l~C~~Cg~~~~C~~C~~~L~~h~ 406 (665)
T PRK14873 381 VPSLACARCRTPARCRHCTGPLGLPS 406 (665)
T ss_pred CCeeEhhhCcCeeECCCCCCceeEec
Confidence 4556777777764 7777664 465
No 130
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=66.97 E-value=1.7 Score=41.64 Aligned_cols=50 Identities=24% Similarity=0.677 Sum_probs=37.6
Q ss_pred cccccccccccccCC-ceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCC
Q 019929 148 GPFVCEICAEQKTVH-KSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGL 204 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 204 (334)
-.+.|..|-+.+-.. +....++|.|.|...|+..|++.. .+-.|| .|...
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-----~~rsCP--~Crkl 414 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-----GTRSCP--NCRKL 414 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-----CCCCCc--cHHHH
Confidence 368899999877542 345567999999999999999532 355899 57743
No 131
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.56 E-value=2.9 Score=23.34 Aligned_cols=22 Identities=50% Similarity=1.180 Sum_probs=12.5
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+|| .|+.-+..+ ...|+.||+.
T Consensus 1 ~Cp--~CG~~~~~~------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDD------AKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCc------CcchhhhCCc
Confidence 466 777654322 2457777654
No 132
>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=66.21 E-value=4.8 Score=29.29 Aligned_cols=25 Identities=24% Similarity=0.775 Sum_probs=19.6
Q ss_pred cccCCCCc----eeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRY----YVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~----~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|+. ..-+..|=.++.|. |||
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy 38 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGY 38 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCC
Confidence 47999987 33456778999995 998
No 133
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=65.93 E-value=4.1 Score=29.97 Aligned_cols=44 Identities=25% Similarity=0.594 Sum_probs=17.5
Q ss_pred cccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeeccCCCc
Q 019929 256 IQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKKDGCMY 327 (334)
Q Consensus 256 ~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~~GCnh 327 (334)
...+.|..|++..|..|. +|. .+.+.+-||.|+++..+..|+-.
T Consensus 26 e~FVAC~eC~fPvCr~Cy----------EYE------------------rkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 26 EVFVACHECAFPVCRPCY----------EYE------------------RKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SB--S-SSS-----HHHH----------HHH------------------HHTS-SB-TTT--B----TT---
T ss_pred CEEEEEcccCCccchhHH----------HHH------------------hhcCcccccccCCCcccccCCCC
Confidence 356889999999888663 232 25778999999999888777643
No 134
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=65.71 E-value=3.3 Score=26.93 Aligned_cols=22 Identities=27% Similarity=0.794 Sum_probs=16.7
Q ss_pred hCCccccCCCCceeeeccCCCceEee
Q 019929 306 KEKWKRCPNCRYYVEKKDGCMYMKCR 331 (334)
Q Consensus 306 ~~~~k~CP~C~~~IeK~~GCnhMtC~ 331 (334)
..+.+.||+|++.- |+--+.|+
T Consensus 8 lRGirkCp~CGt~N----G~R~~~CK 29 (44)
T PF14952_consen 8 LRGIRKCPKCGTYN----GTRGLSCK 29 (44)
T ss_pred HhccccCCcCcCcc----Cccccccc
Confidence 35679999999864 66667774
No 135
>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=65.60 E-value=4.3 Score=27.56 Aligned_cols=25 Identities=20% Similarity=0.149 Sum_probs=16.8
Q ss_pred cccCCCCceee------eccCCCceE-ee-cCC
Q 019929 310 KRCPNCRYYVE------KKDGCMYMK-CR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~Ie------K~~GCnhMt-C~-Cg~ 334 (334)
|+||.|+-.-+ -+.+..++. |. ||+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCC
Confidence 79999998544 234566664 75 874
No 136
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=65.26 E-value=4.7 Score=31.01 Aligned_cols=29 Identities=31% Similarity=0.818 Sum_probs=19.6
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.+|| .|+..++...+.....+.|..|.+.
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPYV 30 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCce
Confidence 4799 8999888876554455666655543
No 137
>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=65.13 E-value=6.4 Score=23.05 Aligned_cols=21 Identities=24% Similarity=0.760 Sum_probs=13.5
Q ss_pred ccCCCCceeeeccCCCceEee
Q 019929 311 RCPNCRYYVEKKDGCMYMKCR 331 (334)
Q Consensus 311 ~CP~C~~~IeK~~GCnhMtC~ 331 (334)
.||.|+..+.+..|=-+..|.
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 599999999998887777774
No 138
>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=64.98 E-value=3.2 Score=24.86 Aligned_cols=24 Identities=25% Similarity=0.577 Sum_probs=10.1
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-+||.|+.-..-.+|.. |.|. |||
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGH 27 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccc
Confidence 36888888777777765 4474 775
No 139
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.75 E-value=5.8 Score=25.94 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=7.3
Q ss_pred CccccCCCCceee
Q 019929 308 KWKRCPNCRYYVE 320 (334)
Q Consensus 308 ~~k~CP~C~~~Ie 320 (334)
...+||.|+..|.
T Consensus 18 ~~irC~~CG~rIl 30 (44)
T smart00659 18 DVVRCRECGYRIL 30 (44)
T ss_pred CceECCCCCceEE
Confidence 3456666666543
No 140
>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=63.70 E-value=4.1 Score=24.77 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=6.4
Q ss_pred CccccCCCCcee
Q 019929 308 KWKRCPNCRYYV 319 (334)
Q Consensus 308 ~~k~CP~C~~~I 319 (334)
...+||.|+..|
T Consensus 16 ~~irC~~CG~RI 27 (32)
T PF03604_consen 16 DPIRCPECGHRI 27 (32)
T ss_dssp STSSBSSSS-SE
T ss_pred CcEECCcCCCeE
Confidence 335677666654
No 141
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.06 E-value=2.9 Score=35.21 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.3
Q ss_pred ccccccccccccccCCceeEecCCCCccc
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYC 175 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC 175 (334)
....+|.||+|++...+.+..|+|-..|.
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEee
Confidence 45789999999999888888889987664
No 142
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=63.02 E-value=1.1 Score=29.96 Aligned_cols=36 Identities=14% Similarity=0.469 Sum_probs=29.3
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHH
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYV 183 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~ 183 (334)
..+.|.+|-+.++..+.-...-||..-|..||+.-+
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhH
Confidence 368999999998877765555799999999998633
No 143
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=62.67 E-value=3.9 Score=23.41 Aligned_cols=23 Identities=39% Similarity=1.016 Sum_probs=13.0
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+.|| .|+..+..+ ...|+.||..
T Consensus 3 ~~Cp--~Cg~~~~~~------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPD------AKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCcc------cccChhhCCC
Confidence 4677 787743221 2567777653
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=62.18 E-value=5.1 Score=43.13 Aligned_cols=27 Identities=22% Similarity=0.629 Sum_probs=17.8
Q ss_pred cccCCccccc----cccccCccCCCCCCchh
Q 019929 258 ESECPNCRRL----FCAQCQVPWHSGINCVE 284 (334)
Q Consensus 258 ~~~C~~C~~~----fC~~C~~~~H~~~tC~~ 284 (334)
..+|+.||.. +|..|+........|..
T Consensus 626 ~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~ 656 (1121)
T PRK04023 626 RRKCPSCGKETFYRRCPFCGTHTEPVYRCPR 656 (1121)
T ss_pred CccCCCCCCcCCcccCCCCCCCCCcceeCcc
Confidence 4689999976 68888875333334443
No 145
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.15 E-value=11 Score=35.17 Aligned_cols=57 Identities=18% Similarity=0.413 Sum_probs=40.4
Q ss_pred CccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchh
Q 019929 146 VYGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 146 ~~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 208 (334)
-.+.|.||+=-+.....++..++.|||.+=..=+...- .+|...++|| -|+..-...
T Consensus 333 fHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~~~FKCP--YCP~~~~~~ 389 (396)
T COG5109 333 FHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGVLSFKCP--YCPEMSKYE 389 (396)
T ss_pred ccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCcEEeeCC--CCCcchhhh
Confidence 35689999977666555666677999999877554432 3577899999 587654443
No 146
>PF14149 YhfH: YhfH-like protein
Probab=61.82 E-value=1.1 Score=28.17 Aligned_cols=28 Identities=21% Similarity=0.500 Sum_probs=22.7
Q ss_pred HHHhCCccccCCCCceeeeccCCCceEe
Q 019929 303 VAQKEKWKRCPNCRYYVEKKDGCMYMKC 330 (334)
Q Consensus 303 ~~~~~~~k~CP~C~~~IeK~~GCnhMtC 330 (334)
+.++...|.||.|+..|+--.-|..++|
T Consensus 7 FfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 3445677999999999998888888877
No 147
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=60.76 E-value=6 Score=30.75 Aligned_cols=28 Identities=25% Similarity=0.485 Sum_probs=19.7
Q ss_pred CCccccCCCCce---eeeccCCCceEee-cCC
Q 019929 307 EKWKRCPNCRYY---VEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 307 ~~~k~CP~C~~~---IeK~~GCnhMtC~-Cg~ 334 (334)
...-.||+|+.. |....|=-|..|. |||
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~ 50 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGL 50 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCC
Confidence 455789999942 2234467799995 997
No 148
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=60.68 E-value=6.8 Score=34.21 Aligned_cols=65 Identities=23% Similarity=0.486 Sum_probs=34.7
Q ss_pred CCcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccC
Q 019929 234 AQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCP 313 (334)
Q Consensus 234 ~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP 313 (334)
.+.+.|| -|...+.. . +. ..|++.||+.|...|.... ..... ....+........||
T Consensus 16 ~~~~~Cp--ICld~~~d------P-Vv-T~CGH~FC~~CI~~wl~~s--~~s~~-----------~~~~~~~~k~~~~CP 72 (193)
T PLN03208 16 GGDFDCN--ICLDQVRD------P-VV-TLCGHLFCWPCIHKWTYAS--NNSRQ-----------RVDQYDHKREPPKCP 72 (193)
T ss_pred CCccCCc--cCCCcCCC------c-EE-cCCCchhHHHHHHHHHHhc--ccccc-----------ccccccccCCCCcCC
Confidence 3446788 66553211 1 22 4699999999987663210 00000 000001123457999
Q ss_pred CCCceeee
Q 019929 314 NCRYYVEK 321 (334)
Q Consensus 314 ~C~~~IeK 321 (334)
-|+..|..
T Consensus 73 vCR~~Is~ 80 (193)
T PLN03208 73 VCKSDVSE 80 (193)
T ss_pred CCCCcCCh
Confidence 99998864
No 149
>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=60.52 E-value=4.6 Score=26.21 Aligned_cols=41 Identities=29% Similarity=0.653 Sum_probs=19.9
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecC
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCP 197 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 197 (334)
|.+|-+-......-....|+=.+...|+..|+..+-. -.||
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~-----~~CP 41 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSN-----PKCP 41 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS------B-T
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCC-----CCCc
Confidence 5677766554333323368889999999999976422 2788
No 150
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=60.26 E-value=6 Score=31.52 Aligned_cols=29 Identities=21% Similarity=0.596 Sum_probs=21.1
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.+|| .|+.++++..........|++|++.
T Consensus 3 ~FCp--~Cgsll~p~~~~~~~~l~C~kCgye 31 (113)
T COG1594 3 RFCP--KCGSLLYPKKDDEGGKLVCRKCGYE 31 (113)
T ss_pred cccC--CccCeeEEeEcCCCcEEECCCCCcc
Confidence 5899 9999998864433346788877764
No 151
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.41 E-value=8.1 Score=35.77 Aligned_cols=31 Identities=26% Similarity=0.674 Sum_probs=23.4
Q ss_pred ccccccccccccCCceeEecCCCCc-ccHHHHHHH
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHA-YCTDCMVKY 182 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~~ 182 (334)
...|.|||+- +.+.| +|+|||. -|..|-+.+
T Consensus 300 ~~LC~ICmDa--P~DCv-fLeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCV-FLECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHHhcC--CcceE-EeecCcEEeehhhcccc
Confidence 6789999985 33655 4699998 788886553
No 152
>PHA02926 zinc finger-like protein; Provisional
Probab=59.24 E-value=2.2 Score=37.95 Aligned_cols=76 Identities=18% Similarity=0.431 Sum_probs=40.0
Q ss_pred hHHHHHHHHHHHHhhcCCCCcccCCCCCCCceEEcCC-ccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhh
Q 019929 216 QDVFDRWGAALCEAVIPGAQKFYCPFKDCSAMLIDDG-EEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDERE 294 (334)
Q Consensus 216 ~~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~-~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~ 294 (334)
+.++.+|+..... +....|+ =|-..+.... ........=+.|++.||+.|-..|....
T Consensus 155 ~~il~~ye~~~~~-----SkE~eCg--ICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r-------------- 213 (242)
T PHA02926 155 IKILDKYEDVYRV-----SKEKECG--ICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTR-------------- 213 (242)
T ss_pred hHHHHHHHHHHhc-----cCCCCCc--cCccccccccccccccccccCCCCchHHHHHHHHHHHhc--------------
Confidence 4566677654432 2334565 5554332211 0011112224799999999966443311
Q ss_pred HHHHHHHHHHHhCCccccCCCCceeee
Q 019929 295 REDILLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 295 ~~d~~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
......+.||-|+..+..
T Consensus 214 ---------~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 214 ---------RETGASDNCPICRTRFRN 231 (242)
T ss_pred ---------cccCcCCcCCCCcceeee
Confidence 012345789999987653
No 153
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=59.03 E-value=4.6 Score=37.26 Aligned_cols=17 Identities=24% Similarity=0.788 Sum_probs=13.5
Q ss_pred ccCCccccccccccCcc
Q 019929 259 SECPNCRRLFCAQCQVP 275 (334)
Q Consensus 259 ~~C~~C~~~fC~~C~~~ 275 (334)
-.|.-||+.||+.|-.+
T Consensus 252 pSaTpCGHiFCWsCI~~ 268 (293)
T KOG0317|consen 252 PSATPCGHIFCWSCILE 268 (293)
T ss_pred CCcCcCcchHHHHHHHH
Confidence 45678999999999654
No 154
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=58.32 E-value=23 Score=29.01 Aligned_cols=53 Identities=19% Similarity=0.468 Sum_probs=38.5
Q ss_pred cccccccccccccCCceeE-ecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 148 GPFVCEICAEQKTVHKSFH-IKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
.-.+|.||-|......+.. -.-||-.+|.-|..+.|+..- ..-.|| -|+..+.
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCP--vCkTSFK 132 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCP--VCKTSFK 132 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCC--ccccccc
Confidence 5789999998765433321 236999999999999998643 345899 4877654
No 155
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=58.10 E-value=10 Score=25.98 Aligned_cols=33 Identities=21% Similarity=0.477 Sum_probs=27.3
Q ss_pred cccccccccccc-CCceeEecCCCCcccHHHHHH
Q 019929 149 PFVCEICAEQKT-VHKSFHIKGCSHAYCTDCMVK 181 (334)
Q Consensus 149 ~~~C~IC~e~~~-~~~~~~~~~C~H~fC~~Cl~~ 181 (334)
...|++|-+.|. ..+.+....|+-.+.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999986 456677789999999999965
No 156
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=57.84 E-value=6.5 Score=43.40 Aligned_cols=50 Identities=18% Similarity=0.458 Sum_probs=30.5
Q ss_pred cccCCcccc----ccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceee
Q 019929 258 ESECPNCRR----LFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVE 320 (334)
Q Consensus 258 ~~~C~~C~~----~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~Ie 320 (334)
...||.||. .||..|+........|..-...... ....+..||+|+.+..
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~-------------des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPP-------------DESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCceeCccCCCccCC-------------CccccccCCCCCCccc
Confidence 478999996 4899999876444456543211000 0112568998887654
No 157
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.32 E-value=9.8 Score=35.06 Aligned_cols=54 Identities=20% Similarity=0.498 Sum_probs=38.5
Q ss_pred ccccccccccccccCCceeEec-CCCCcccHHHHHHHHHhhhhCCeeeeecCC-CcCC
Q 019929 147 YGPFVCEICAEQKTVHKSFHIK-GCSHAYCTDCMVKYVAAKLEENITAIRCPV-VDCR 202 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~-~~C~ 202 (334)
...+-|.+|-+.+....++... -=.|.||..|-++.|+.+-..+ .+.||. ..|.
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg--evYCPSGdkCP 321 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG--EVYCPSGDKCP 321 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC--ceeCCCCCcCc
Confidence 4568999999987654433321 1269999999999999875444 778997 3464
No 158
>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=56.78 E-value=9.4 Score=24.56 Aligned_cols=23 Identities=22% Similarity=0.423 Sum_probs=10.3
Q ss_pred ccCCCCce-eeeccCCCceEee-cC
Q 019929 311 RCPNCRYY-VEKKDGCMYMKCR-SV 333 (334)
Q Consensus 311 ~CP~C~~~-IeK~~GCnhMtC~-Cg 333 (334)
.||.|+.. |.-+..=.-+.|+ ||
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 36666653 3333333344553 55
No 159
>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=56.69 E-value=7.6 Score=21.97 Aligned_cols=9 Identities=44% Similarity=0.833 Sum_probs=5.7
Q ss_pred CccccCCCC
Q 019929 308 KWKRCPNCR 316 (334)
Q Consensus 308 ~~k~CP~C~ 316 (334)
..-.||+|+
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345777776
No 160
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.35 E-value=6.6 Score=39.09 Aligned_cols=35 Identities=29% Similarity=0.649 Sum_probs=24.6
Q ss_pred ccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeee
Q 019929 263 NCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 263 ~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
.||+.||+.|... -|. +.....++.||-|...|-.
T Consensus 203 ~CGHiFC~~CiLq-----------y~~-------------~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQ-----------YWN-------------YSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHH-----------HHh-------------hhcccCCccCCchhhhccc
Confidence 5999999999642 121 1124678999999988754
No 161
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=55.29 E-value=6.9 Score=27.14 Aligned_cols=24 Identities=21% Similarity=0.364 Sum_probs=19.0
Q ss_pred hCCccccCCCCceeeeccCCCceEe-ecCC
Q 019929 306 KEKWKRCPNCRYYVEKKDGCMYMKC-RSVF 334 (334)
Q Consensus 306 ~~~~k~CP~C~~~IeK~~GCnhMtC-~Cg~ 334 (334)
..+.-.||+|+.++.. |-.| .|||
T Consensus 24 ~~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC-----eEECCCCCc
Confidence 4556789999998764 8889 4987
No 162
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=54.94 E-value=3.9 Score=27.71 Aligned_cols=23 Identities=35% Similarity=0.949 Sum_probs=13.5
Q ss_pred ccccCCccccccccccCccCCCC
Q 019929 257 QESECPNCRRLFCAQCQVPWHSG 279 (334)
Q Consensus 257 ~~~~C~~C~~~fC~~C~~~~H~~ 279 (334)
....|+.|+..||+.|-.-.|.-
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 56899999999999986655553
No 163
>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=53.67 E-value=14 Score=25.32 Aligned_cols=30 Identities=30% Similarity=0.623 Sum_probs=21.3
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
+.|| .|+.-+..........+.|+.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4688 99988776544334568899888754
No 164
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=53.63 E-value=3.3 Score=38.72 Aligned_cols=26 Identities=27% Similarity=0.493 Sum_probs=11.3
Q ss_pred ccccCCCCceeeecc-CCCceEee-cCC
Q 019929 309 WKRCPNCRYYVEKKD-GCMYMKCR-SVF 334 (334)
Q Consensus 309 ~k~CP~C~~~IeK~~-GCnhMtC~-Cg~ 334 (334)
|.+||+|+..|.+.. .=|.+.|+ |||
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGY 65 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCC
Confidence 455555555444322 23344443 443
No 165
>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=52.88 E-value=9.2 Score=27.22 Aligned_cols=17 Identities=29% Similarity=0.854 Sum_probs=12.5
Q ss_pred cccHHHHHHHHHhhhhC
Q 019929 173 AYCTDCMVKYVAAKLEE 189 (334)
Q Consensus 173 ~fC~~Cl~~~~~~~i~~ 189 (334)
-||+.||..|+.....+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999887654
No 166
>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=52.75 E-value=13 Score=23.55 Aligned_cols=21 Identities=33% Similarity=0.961 Sum_probs=14.1
Q ss_pred cccCCCCc-eeee--ccCCCceEee
Q 019929 310 KRCPNCRY-YVEK--KDGCMYMKCR 331 (334)
Q Consensus 310 k~CP~C~~-~IeK--~~GCnhMtC~ 331 (334)
+.||.|+. +|+| ..| ..+.|+
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 57999998 4444 335 666673
No 167
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.84 E-value=18 Score=32.24 Aligned_cols=54 Identities=17% Similarity=0.391 Sum_probs=39.3
Q ss_pred cccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCC-eeeeecCCCcCCCCCc
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEEN-ITAIRCPVVDCRGLLE 206 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~ 206 (334)
-.|.+|-..+...+...+ .|-|.|.-.|+..+...--.+. -....|| .|...|-
T Consensus 51 pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP--~Cs~eiF 105 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCP--CCSQEIF 105 (299)
T ss_pred CCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCC--CCCCccC
Confidence 459999988887787765 8999999999998865433321 2446899 6876443
No 168
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=51.05 E-value=12 Score=25.93 Aligned_cols=25 Identities=28% Similarity=0.612 Sum_probs=15.3
Q ss_pred ccccCCCCceeee--c-cC--C---CceEee-cC
Q 019929 309 WKRCPNCRYYVEK--K-DG--C---MYMKCR-SV 333 (334)
Q Consensus 309 ~k~CP~C~~~IeK--~-~G--C---nhMtC~-Cg 333 (334)
.|+||.|+..... . .| - ..|.|. ||
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cg 36 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCG 36 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCC
Confidence 5899999863322 2 22 1 467785 87
No 169
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.62 E-value=5.3 Score=40.80 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=27.1
Q ss_pred ccccccccccccCCce-eEecCCCCcccHHHHHHHHHh
Q 019929 149 PFVCEICAEQKTVHKS-FHIKGCSHAYCTDCMVKYVAA 185 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~ 185 (334)
...|+||+..|-.... ...+.|||..|+.|+......
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 5679999887754332 223589999999999877643
No 170
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=49.99 E-value=14 Score=30.53 Aligned_cols=14 Identities=14% Similarity=0.325 Sum_probs=11.2
Q ss_pred CccccCCCCceeee
Q 019929 308 KWKRCPNCRYYVEK 321 (334)
Q Consensus 308 ~~k~CP~C~~~IeK 321 (334)
..-+|.+|+.+|..
T Consensus 80 l~~~CE~CG~~I~~ 93 (137)
T TIGR03826 80 LGYPCERCGTSIRE 93 (137)
T ss_pred CcCcccccCCcCCC
Confidence 34799999999864
No 171
>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=48.74 E-value=13 Score=25.52 Aligned_cols=45 Identities=29% Similarity=0.666 Sum_probs=29.7
Q ss_pred cccccccccccCCceeEecCCC--CcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 150 FVCEICAEQKTVHKSFHIKGCS--HAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
-.|..|-.+++....-.. -|. ..||.+|....+.. .|| .|+..|.
T Consensus 6 pnCE~C~~dLp~~s~~A~-ICSfECTFC~~C~e~~l~~---------~CP--NCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAY-ICSFECTFCADCAETMLNG---------VCP--NCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcce-EEeEeCcccHHHHHHHhcC---------cCc--CCCCccc
Confidence 358888888876542111 244 56999999887632 689 5876554
No 172
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.71 E-value=13 Score=33.71 Aligned_cols=39 Identities=10% Similarity=0.166 Sum_probs=29.9
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhC
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEE 189 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 189 (334)
+..-|.+|+..+. +++. .+=||.||++|+.+||..+-++
T Consensus 42 ~FdcCsLtLqPc~--dPvi-t~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 42 PFDCCSLTLQPCR--DPVI-TPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred Ccceeeeeccccc--CCcc-CCCCeeeeHHHHHHHHHHHHHH
Confidence 3556888998776 4454 4789999999999999877543
No 173
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=48.55 E-value=7.9 Score=35.77 Aligned_cols=47 Identities=23% Similarity=0.565 Sum_probs=35.2
Q ss_pred cccccccccccccCCc-eeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 148 GPFVCEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
..+.||||.+.+.... ....+.|||..-..|++.+... + ..|| -|..
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~----~---y~CP--~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE----G---YTCP--ICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc----C---CCCC--cccc
Confidence 4566999998765433 3446799999999999988753 2 5899 5877
No 174
>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=48.33 E-value=26 Score=29.59 Aligned_cols=37 Identities=27% Similarity=0.705 Sum_probs=23.0
Q ss_pred ccccccccccccCCceeEec------CCCCccc------HHHHHHHHHhhh
Q 019929 149 PFVCEICAEQKTVHKSFHIK------GCSHAYC------TDCMVKYVAAKL 187 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~------~C~H~fC------~~Cl~~~~~~~i 187 (334)
...|+||++. + .+.+-++ +|.-++| .+||.+|-+...
T Consensus 2 d~~CpICme~-P-HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEH-P-HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccC-C-CceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 4679999985 2 2333221 4555566 478988877654
No 175
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=47.95 E-value=13 Score=38.62 Aligned_cols=32 Identities=25% Similarity=0.791 Sum_probs=21.3
Q ss_pred CcccCCCCCCCceEEcCCccccccccCCccccc------cccccCccC
Q 019929 235 QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL------FCAQCQVPW 276 (334)
Q Consensus 235 ~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~------fC~~C~~~~ 276 (334)
+.++|| .|+..+. ...|+.||.. ||..|+...
T Consensus 14 ~akFC~--~CG~~l~--------~~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 14 NNRFCQ--KCGTSLT--------HKPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCcccc--ccCCCCC--------CCcCCCCCCCCCcccccccccCCcc
Confidence 345788 7775432 1368888765 888888753
No 176
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=47.73 E-value=9.3 Score=24.33 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=13.7
Q ss_pred cCCCCCCCceEEcCCccccccccCCcccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRR 266 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~ 266 (334)
.|| .|+..+..........-.|+.|+-
T Consensus 1 ~CP--~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCP--RCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred CcC--CCCcccceEEECCEEEEECCCCCe
Confidence 367 787654433223334445665554
No 177
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=46.92 E-value=6.9 Score=28.71 Aligned_cols=50 Identities=24% Similarity=0.574 Sum_probs=33.4
Q ss_pred cccccccccccC---------Cce-eEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCC
Q 019929 150 FVCEICAEQKTV---------HKS-FHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLL 205 (334)
Q Consensus 150 ~~C~IC~e~~~~---------~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 205 (334)
.+|.||--.|.. .+. ...--|.|.|-.-|+.+|+.+.-.++ .|| -|.+.+
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~----~CP--mcRq~~ 80 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG----QCP--MCRQTW 80 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc----cCC--cchhee
Confidence 378888766642 221 11225889999999999998776554 688 476654
No 178
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=46.83 E-value=26 Score=25.90 Aligned_cols=51 Identities=22% Similarity=0.591 Sum_probs=20.2
Q ss_pred cccccccccccccC---Ccee-EecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 148 GPFVCEICAEQKTV---HKSF-HIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 148 ~~~~C~IC~e~~~~---~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
....|.||-+++-. .+.| ..-.|+-..|+.|+.--. ++|. -.|| .|+..+.
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~--q~Cp--qCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGN--QVCP--QCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS---SB-T--TT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCc--cccc--ccCCCcc
Confidence 35789999998743 3444 345788899999995433 3442 3788 6875443
No 179
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=46.81 E-value=16 Score=24.15 Aligned_cols=33 Identities=18% Similarity=0.563 Sum_probs=22.2
Q ss_pred cccccccccCCceeEecCCCC-----cccHHHHHHHHHh
Q 019929 152 CEICAEQKTVHKSFHIKGCSH-----AYCTDCMVKYVAA 185 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~ 185 (334)
|-||++.......+. .+|.. .....||..|+..
T Consensus 1 CrIC~~~~~~~~~li-~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLI-SPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE--SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCcee-cccccCCCcchhHHHHHHHHHHh
Confidence 679998766555343 36652 5789999999987
No 180
>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=46.51 E-value=8 Score=24.97 Aligned_cols=18 Identities=28% Similarity=0.916 Sum_probs=12.3
Q ss_pred cccCCccccccccccCcc
Q 019929 258 ESECPNCRRLFCAQCQVP 275 (334)
Q Consensus 258 ~~~C~~C~~~fC~~C~~~ 275 (334)
.+.|+.|+..||...+.+
T Consensus 13 ~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp HEE-TTTS-EE-TTTHST
T ss_pred CeECCCCCcccCccccCc
Confidence 378999999999988764
No 181
>PHA02929 N1R/p28-like protein; Provisional
Probab=45.95 E-value=13 Score=33.70 Aligned_cols=38 Identities=21% Similarity=0.422 Sum_probs=20.3
Q ss_pred cccCCCCCCCceEEcCCccccccccCCccccccccccCcc
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVP 275 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 275 (334)
...|| =|...+............=+.|++.||..|-..
T Consensus 174 ~~eC~--ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~ 211 (238)
T PHA02929 174 DKECA--ICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211 (238)
T ss_pred CCCCc--cCCcccccCccccccceecCCCCCcccHHHHHH
Confidence 45788 676544322110000112246999999999553
No 182
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.65 E-value=25 Score=30.24 Aligned_cols=59 Identities=17% Similarity=0.381 Sum_probs=38.1
Q ss_pred cccccccccccccc----CCceeEecCCCCcccHHHHHHHHHhhhhC----CeeeeecCCCcCCCCCch
Q 019929 147 YGPFVCEICAEQKT----VHKSFHIKGCSHAYCTDCMVKYVAAKLEE----NITAIRCPVVDCRGLLEP 207 (334)
Q Consensus 147 ~~~~~C~IC~e~~~----~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~----~~~~i~CP~~~C~~~l~~ 207 (334)
.....|.||+..-- .....-...||..|..-|+..|+..-+.. ++..=.|| -|..++..
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pial 229 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIAL 229 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCccee
Confidence 34567788875321 11222234799999999999999876644 24445798 58777654
No 183
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.52 E-value=33 Score=36.46 Aligned_cols=42 Identities=24% Similarity=0.604 Sum_probs=30.1
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
+...|..|-..+..+ +....|||.|...|+. ++ .-.|| .|..
T Consensus 839 q~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e--------~~--~~~CP--~C~~ 880 (933)
T KOG2114|consen 839 QVSKCSACEGTLDLP--FVHFLCGHSYHQHCLE--------DK--EDKCP--KCLP 880 (933)
T ss_pred eeeeecccCCccccc--eeeeecccHHHHHhhc--------cC--cccCC--ccch
Confidence 346899998766543 3334799999999998 22 34899 6866
No 184
>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=45.46 E-value=26 Score=23.46 Aligned_cols=47 Identities=19% Similarity=0.509 Sum_probs=24.2
Q ss_pred cccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 150 FVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
+.|+|-+..+. -+.....|.|.-|.+ +..|+......+. ..|| -|..
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~--W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPK--WKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS-----B-T--TT--
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCC--eECc--CCcC
Confidence 56888876654 345567999998865 6678877665543 6899 4654
No 185
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=45.40 E-value=14 Score=32.05 Aligned_cols=24 Identities=29% Similarity=0.450 Sum_probs=19.7
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||.|+.+..+.+. |+|.|+ ||+
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~ 174 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGN 174 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCC
Confidence 379999999988554 999995 985
No 186
>PRK00420 hypothetical protein; Validated
Probab=45.34 E-value=34 Score=27.19 Aligned_cols=44 Identities=20% Similarity=0.345 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhhcCCCCcccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 217 DVFDRWGAALCEAVIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 217 ~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+...+.-+++...+..- ...|| .|+..+..... ...+||.||..
T Consensus 6 ~~~k~~a~~Ll~Ga~ml--~~~CP--~Cg~pLf~lk~---g~~~Cp~Cg~~ 49 (112)
T PRK00420 6 DIVKKAAELLLKGAKML--SKHCP--VCGLPLFELKD---GEVVCPVHGKV 49 (112)
T ss_pred HHHHHHHHHHHhHHHHc--cCCCC--CCCCcceecCC---CceECCCCCCe
Confidence 33444444444433221 25899 79876664211 12677776653
No 187
>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=45.06 E-value=5.7 Score=25.17 Aligned_cols=25 Identities=28% Similarity=0.728 Sum_probs=21.3
Q ss_pred ccccCCccccccccccCccCCCCCC
Q 019929 257 QESECPNCRRLFCAQCQVPWHSGIN 281 (334)
Q Consensus 257 ~~~~C~~C~~~fC~~C~~~~H~~~t 281 (334)
..++|..|+..+|..|....|.++.
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred eEEEecCCCCccCccCCCCCCCCCE
Confidence 4489999999999999988888753
No 188
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=44.81 E-value=10 Score=40.57 Aligned_cols=22 Identities=41% Similarity=0.899 Sum_probs=18.2
Q ss_pred cccCCCCc-eeeeccCCCceEee-cC
Q 019929 310 KRCPNCRY-YVEKKDGCMYMKCR-SV 333 (334)
Q Consensus 310 k~CP~C~~-~IeK~~GCnhMtC~-Cg 333 (334)
-.||-|+. .||..|||| ||+ ||
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~ 851 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCG 851 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchh
Confidence 48999998 889999999 564 54
No 189
>PF14369 zf-RING_3: zinc-finger
Probab=44.70 E-value=27 Score=21.57 Aligned_cols=30 Identities=20% Similarity=0.690 Sum_probs=19.0
Q ss_pred cccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
..||- .|...+....... ..+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~~-~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSPD-SDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCCC-CCcCCcCCCCcE
Confidence 35888 8998877643211 224699887654
No 190
>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=44.15 E-value=11 Score=23.17 Aligned_cols=25 Identities=32% Similarity=0.646 Sum_probs=20.7
Q ss_pred ccccCCccccccccccCccCCCCCC
Q 019929 257 QESECPNCRRLFCAQCQVPWHSGIN 281 (334)
Q Consensus 257 ~~~~C~~C~~~fC~~C~~~~H~~~t 281 (334)
..++|..|+..+|..|....|.++.
T Consensus 11 ~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 11 LSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred eEEEeCccChhhhhhcChhhcCCCC
Confidence 3488999999999999877787664
No 191
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=43.07 E-value=18 Score=37.90 Aligned_cols=47 Identities=28% Similarity=0.575 Sum_probs=34.0
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
..+.|.||.-.+.....+. ..|+|....+|+..||... -.||. +|+-
T Consensus 1027 ~~~~C~~C~l~V~gss~~C-g~C~Hv~H~sc~~eWf~~g-------d~Cps-GCGC 1073 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFC-GTCGHVGHTSCMMEWFRTG-------DVCPS-GCGC 1073 (1081)
T ss_pred ceeeeeeEeeEeeccchhh-ccccccccHHHHHHHHhcC-------CcCCC-CCCc
Confidence 4567888876665555454 4899999999999999863 17886 4443
No 192
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.73 E-value=17 Score=27.37 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=21.4
Q ss_pred CccccCCCCceeeeccCCCceEee-cCC
Q 019929 308 KWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 308 ~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
.--.||.|+....|..+=---.|+ |||
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 346899999999988877777774 876
No 193
>PRK12495 hypothetical protein; Provisional
Probab=42.59 E-value=29 Score=30.92 Aligned_cols=12 Identities=17% Similarity=0.634 Sum_probs=9.3
Q ss_pred cccCCCCCCCceEE
Q 019929 236 KFYCPFKDCSAMLI 249 (334)
Q Consensus 236 ~~~CP~p~C~~~~~ 249 (334)
.++|+ .|+..|+
T Consensus 42 a~hC~--~CG~PIp 53 (226)
T PRK12495 42 NAHCD--ECGDPIF 53 (226)
T ss_pred hhhcc--cccCccc
Confidence 36999 8988766
No 194
>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=42.45 E-value=13 Score=21.87 Aligned_cols=21 Identities=33% Similarity=0.907 Sum_probs=10.7
Q ss_pred cccCCCCceeee--ccCCCceEe
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKC 330 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC 330 (334)
++||+|+..|++ .+|=+...|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C 24 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLC 24 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-
T ss_pred CcCccCCCcceEeEecCCCCeEC
Confidence 589999999976 334333444
No 195
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=42.18 E-value=24 Score=23.84 Aligned_cols=30 Identities=33% Similarity=0.743 Sum_probs=22.2
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHH
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKY 182 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~ 182 (334)
.|.||.........+.+ .=| +.|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 49999988765444444 566 8999999876
No 196
>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=41.06 E-value=16 Score=19.00 Aligned_cols=16 Identities=31% Similarity=0.687 Sum_probs=13.1
Q ss_pred cccccCccCCCCCCch
Q 019929 268 FCAQCQVPWHSGINCV 283 (334)
Q Consensus 268 fC~~C~~~~H~~~tC~ 283 (334)
.|++|+..-|.-..|.
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 5899999999877774
No 197
>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=40.73 E-value=9.1 Score=40.56 Aligned_cols=16 Identities=31% Similarity=1.167 Sum_probs=0.0
Q ss_pred ccCCccccc-----cccccCc
Q 019929 259 SECPNCRRL-----FCAQCQV 274 (334)
Q Consensus 259 ~~C~~C~~~-----fC~~C~~ 274 (334)
..|+.||.. +|..|+.
T Consensus 668 ~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 668 NRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp ---------------------
T ss_pred hcCcccCCccccceecccccc
Confidence 455556544 4555554
No 198
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=40.45 E-value=7.6 Score=36.21 Aligned_cols=49 Identities=24% Similarity=0.640 Sum_probs=31.1
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCC
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCR 316 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~ 316 (334)
-+|- .|..-|..-. +.+ -|+++||+.|-. ....|-||.|.
T Consensus 91 HfCd--~Cd~PI~IYG----RmI---PCkHvFCl~CAr-------------------------------~~~dK~Cp~C~ 130 (389)
T KOG2932|consen 91 HFCD--RCDFPIAIYG----RMI---PCKHVFCLECAR-------------------------------SDSDKICPLCD 130 (389)
T ss_pred Eeec--ccCCcceeee----ccc---ccchhhhhhhhh-------------------------------cCccccCcCcc
Confidence 3777 7776443221 112 389999999954 11247888888
Q ss_pred ceeeeccCC
Q 019929 317 YYVEKKDGC 325 (334)
Q Consensus 317 ~~IeK~~GC 325 (334)
-.|+|.+-|
T Consensus 131 d~VqrIeq~ 139 (389)
T KOG2932|consen 131 DRVQRIEQI 139 (389)
T ss_pred cHHHHHHHh
Confidence 888877655
No 199
>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=40.24 E-value=16 Score=25.84 Aligned_cols=37 Identities=19% Similarity=0.613 Sum_probs=19.3
Q ss_pred ccccccccccccccCC-ceeEecCCCCcccHHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVH-KSFHIKGCSHAYCTDCMVKYV 183 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~-~~~~~~~C~H~fC~~Cl~~~~ 183 (334)
.+...|.+|...|... .......||+.||..|....+
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 3457799999988653 234456899999999986544
No 200
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=40.18 E-value=26 Score=27.21 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=20.2
Q ss_pred CCCcccCCCCCCCceEEc-CCccccccccCCcccccc
Q 019929 233 GAQKFYCPFKDCSAMLID-DGEEVIQESECPNCRRLF 268 (334)
Q Consensus 233 ~~~~~~CP~p~C~~~~~~-~~~~~~~~~~C~~C~~~f 268 (334)
.+..+.|| .|+..... ........+.|+.||+.+
T Consensus 18 lpt~f~CP--~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECP--RCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECC--CCCCeEeeeecCCCcceEECCCCCCcc
Confidence 45667899 78843322 111134457888888764
No 201
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=39.47 E-value=21 Score=32.29 Aligned_cols=57 Identities=14% Similarity=0.249 Sum_probs=35.1
Q ss_pred hhhccCChHHHHHHHHHHHHh-hcC--CCCcccCCCCCCCceEEcCCc----cccccccCCccccc
Q 019929 209 YCRDILPQDVFDRWGAALCEA-VIP--GAQKFYCPFKDCSAMLIDDGE----EVIQESECPNCRRL 267 (334)
Q Consensus 209 ~i~~ll~~~~~~~y~~~~~~~-~~~--~~~~~~CP~p~C~~~~~~~~~----~~~~~~~C~~C~~~ 267 (334)
.+..-++++++..|++..... -.. .-...-|- +|...+..... .....++||.||..
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 456678899999999887654 111 11223687 88876654311 12345889988753
No 202
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=38.01 E-value=19 Score=24.15 Aligned_cols=15 Identities=27% Similarity=0.605 Sum_probs=9.6
Q ss_pred hCCccccCCCCceee
Q 019929 306 KEKWKRCPNCRYYVE 320 (334)
Q Consensus 306 ~~~~k~CP~C~~~Ie 320 (334)
.....+||.|+..|.
T Consensus 21 ~~~~irCp~Cg~rIl 35 (49)
T COG1996 21 ETRGIRCPYCGSRIL 35 (49)
T ss_pred ccCceeCCCCCcEEE
Confidence 344467888877653
No 203
>smart00336 BBOX B-Box-type zinc finger.
Probab=37.59 E-value=20 Score=22.33 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=19.9
Q ss_pred cccCCccccccccccCccCCCCCC
Q 019929 258 ESECPNCRRLFCAQCQVPWHSGIN 281 (334)
Q Consensus 258 ~~~C~~C~~~fC~~C~~~~H~~~t 281 (334)
.++|..|....|..|....|.++.
T Consensus 15 ~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 15 EFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred EEECCCCCcccccccChhhcCCCc
Confidence 478999999999999977787653
No 204
>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=37.52 E-value=24 Score=25.51 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=11.2
Q ss_pred ccCCCCceeeeccCCCceEe
Q 019929 311 RCPNCRYYVEKKDGCMYMKC 330 (334)
Q Consensus 311 ~CP~C~~~IeK~~GCnhMtC 330 (334)
.||.|+..++..+ .+..|
T Consensus 3 ~CP~C~~~L~~~~--~~~~C 20 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHC 20 (70)
T ss_dssp B-SSS-SBEEEET--TEEEE
T ss_pred cCCCCCCccEEeC--CEEEC
Confidence 5888888877777 45555
No 205
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.35 E-value=5 Score=37.36 Aligned_cols=87 Identities=21% Similarity=0.437 Sum_probs=45.5
Q ss_pred CCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHHHHH-HHhhcCCC-----CcccCCCCCC
Q 019929 171 SHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWGAAL-CEAVIPGA-----QKFYCPFKDC 244 (334)
Q Consensus 171 ~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~~~~-~~~~~~~~-----~~~~CP~p~C 244 (334)
|-++|..|-..... .+|.|| .|...+ +|+-.+...|..++ ++.+.+.+ ....|- .|
T Consensus 307 gGy~CP~CktkVCs-------LPi~CP--~Csl~L-------ilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~C 368 (421)
T COG5151 307 GGYECPVCKTKVCS-------LPISCP--ICSLQL-------ILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VC 368 (421)
T ss_pred CceeCCcccceeec-------CCccCc--chhHHH-------HHHHHHHHHHHhhccCcccccccCCCCCCCccce--ec
Confidence 34566666433322 577888 454322 33344555555443 12222211 112465 56
Q ss_pred CceEEcC------CccccccccCCccccccccccCcc
Q 019929 245 SAMLIDD------GEEVIQESECPNCRRLFCAQCQVP 275 (334)
Q Consensus 245 ~~~~~~~------~~~~~~~~~C~~C~~~fC~~C~~~ 275 (334)
+..+... ........+|+.|+..||..|..-
T Consensus 369 Q~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvf 405 (421)
T COG5151 369 QGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVF 405 (421)
T ss_pred cCCCCCCCCCcccccccccceechhhhhhhhhhhHHH
Confidence 6644332 122345688999999999988653
No 206
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=37.28 E-value=30 Score=32.60 Aligned_cols=42 Identities=26% Similarity=0.852 Sum_probs=28.4
Q ss_pred cccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCC
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCR 202 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 202 (334)
|-.|.++......+....|.+.||.+|=. |+...+. .|| +|.
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv-~iHesLh------~Cp--gCe 374 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCDV-FIHESLH------NCP--GCE 374 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccchH-HHHhhhh------cCC--CcC
Confidence 77776666555667777899999999963 4433332 688 565
No 207
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.21 E-value=22 Score=26.97 Aligned_cols=17 Identities=18% Similarity=0.737 Sum_probs=14.4
Q ss_pred cccHHHHHHHHHhhhhC
Q 019929 173 AYCTDCMVKYVAAKLEE 189 (334)
Q Consensus 173 ~fC~~Cl~~~~~~~i~~ 189 (334)
-||+.|+..|+......
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887654
No 208
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=36.90 E-value=56 Score=21.21 Aligned_cols=25 Identities=16% Similarity=0.281 Sum_probs=15.0
Q ss_pred cccCCCCce-eeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYY-VEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~-IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|+.. +-...+=....|. |++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 569999983 3344444455563 653
No 209
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=36.88 E-value=19 Score=41.60 Aligned_cols=23 Identities=26% Similarity=0.714 Sum_probs=20.2
Q ss_pred cccCCCCce------eeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYY------VEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~------IeK~~GCnhMtC~-Cg~ 334 (334)
..||-|+.. +.-.+||. +|+ |||
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~ 1734 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGW 1734 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCC
Confidence 349999999 88899997 896 998
No 210
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=36.80 E-value=22 Score=28.04 Aligned_cols=27 Identities=33% Similarity=0.731 Sum_probs=15.5
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
+.|| .|+.-|.-=. + ..+.||+||..|
T Consensus 10 R~Cp--~CG~kFYDLn--k-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCP--SCGAKFYDLN--K-DPIVCPKCGTEF 36 (108)
T ss_pred ccCC--CCcchhccCC--C-CCccCCCCCCcc
Confidence 4687 7776443211 1 236788877765
No 211
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=36.67 E-value=31 Score=31.56 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=23.8
Q ss_pred HHHHHHhCCccccCCCCceeeeccCCCceEee-cCC
Q 019929 300 LMKVAQKEKWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 300 ~~~~~~~~~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
+..|. ...+.||.|+..++...|=..+.|. ||+
T Consensus 92 l~~w~--~~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 92 LAEFY--RSHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred HHHHh--hcCccccccCCCCeecCCceeEECCCCCC
Confidence 34443 4569999999988775555778895 874
No 212
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=36.37 E-value=25 Score=29.67 Aligned_cols=30 Identities=20% Similarity=0.479 Sum_probs=19.0
Q ss_pred CcccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 235 QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 235 ~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
....|| .|..-+.....- ...+.||.||..
T Consensus 108 ~~Y~Cp--~c~~r~tf~eA~-~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICP--NMCVRFTFNEAM-ELNFTCPRCGAM 137 (158)
T ss_pred CeEECC--CCCcEeeHHHHH-HcCCcCCCCCCE
Confidence 345798 788666554322 235889988764
No 213
>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=36.28 E-value=28 Score=21.65 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=17.0
Q ss_pred ccCCCCCCCceEEcCCc-cccccccCCcccc
Q 019929 237 FYCPFKDCSAMLIDDGE-EVIQESECPNCRR 266 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~-~~~~~~~C~~C~~ 266 (334)
+.|+ .|+..+..... .......||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4687 89885543321 1134578888875
No 214
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=36.16 E-value=28 Score=27.53 Aligned_cols=18 Identities=11% Similarity=0.229 Sum_probs=11.5
Q ss_pred eeecCCCcCCCCCchhhhhc
Q 019929 193 AIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 193 ~i~CP~~~C~~~l~~~~i~~ 212 (334)
.+.|+ .|+..++...+..
T Consensus 25 ~~~C~--~Ck~~~~v~~~~~ 42 (116)
T KOG2907|consen 25 TVLCI--RCKIEYPVSQFSG 42 (116)
T ss_pred ceEec--cccccCCHHHhCC
Confidence 34477 6887777765544
No 215
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=35.86 E-value=27 Score=29.04 Aligned_cols=32 Identities=19% Similarity=0.492 Sum_probs=18.7
Q ss_pred CCcccCCCCCCCceEEcCCc----cccccccCCccccc
Q 019929 234 AQKFYCPFKDCSAMLIDDGE----EVIQESECPNCRRL 267 (334)
Q Consensus 234 ~~~~~CP~p~C~~~~~~~~~----~~~~~~~C~~C~~~ 267 (334)
...+.|| .|+..+..... +....+.||.||..
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 3445899 79876655311 11223788877754
No 216
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=34.66 E-value=42 Score=23.38 Aligned_cols=32 Identities=16% Similarity=0.375 Sum_probs=21.6
Q ss_pred cccccccccCCceeEecCCCCcccHH----HHHHHHHh
Q 019929 152 CEICAEQKTVHKSFHIKGCSHAYCTD----CMVKYVAA 185 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~fC~~----Cl~~~~~~ 185 (334)
|..|... ..+.+..|.|++.+|.. ....|++.
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~ 36 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYKE 36 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhcc
Confidence 5666644 34667778999999996 77777763
No 217
>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=34.56 E-value=20 Score=24.17 Aligned_cols=40 Identities=18% Similarity=0.480 Sum_probs=22.8
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCC
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLL 205 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 205 (334)
.|.||.|...++... |..++...=......+.|| -|...+
T Consensus 2 ~f~CP~C~~~~~~~~---------------L~~H~~~~H~~~~~~v~CP--iC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSESS---------------LVEHCEDEHRSESKNVVCP--ICSSRV 41 (54)
T ss_pred CcCCCCCCCccCHHH---------------HHHHHHhHCcCCCCCccCC--Cchhhh
Confidence 578999987543211 2344444333333468999 576543
No 218
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=34.19 E-value=26 Score=38.36 Aligned_cols=57 Identities=18% Similarity=0.447 Sum_probs=38.4
Q ss_pred CCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeec
Q 019929 243 DCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKK 322 (334)
Q Consensus 243 ~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~ 322 (334)
-|+.-+-.. .+....+-|..|++..|..|.+ |.+ +.+.+-||+|++...+-
T Consensus 22 ICGD~vg~~-~~Ge~FVAC~eC~FPVCrpCYE----------YEr------------------~eG~q~CPqCktrYkr~ 72 (1079)
T PLN02638 22 ICGDNVGKT-VDGEPFVACDVCAFPVCRPCYE----------YER------------------KDGNQSCPQCKTKYKRH 72 (1079)
T ss_pred ecccccCcC-CCCCEEEEeccCCCccccchhh----------hhh------------------hcCCccCCccCCchhhh
Confidence 455443332 2233568999999999987743 322 46679999999988877
Q ss_pred cCCCce
Q 019929 323 DGCMYM 328 (334)
Q Consensus 323 ~GCnhM 328 (334)
-|+..+
T Consensus 73 kgsprv 78 (1079)
T PLN02638 73 KGSPAI 78 (1079)
T ss_pred cCCCCc
Confidence 777643
No 219
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=34.10 E-value=18 Score=35.35 Aligned_cols=68 Identities=16% Similarity=0.321 Sum_probs=35.2
Q ss_pred cccccCCccccc----cccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceee-e--ccCC---
Q 019929 256 IQESECPNCRRL----FCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVE-K--KDGC--- 325 (334)
Q Consensus 256 ~~~~~C~~C~~~----fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~Ie-K--~~GC--- 325 (334)
.+.+.|-.+-+. -|..|..+.-..--+++..+...-.+ ++ ..+--+|-.|+..+. + ..||
T Consensus 380 ~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr--------~f--Hv~CY~CEDCg~~LS~e~e~qgCyPl 449 (468)
T KOG1701|consen 380 QNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDR--------DF--HVNCYKCEDCGLLLSSEEEGQGCYPL 449 (468)
T ss_pred CCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccc--------cc--cccceehhhcCccccccCCCCcceec
Confidence 345777555322 37777776544434443222111000 00 233457777888766 3 4567
Q ss_pred -CceEee-cC
Q 019929 326 -MYMKCR-SV 333 (334)
Q Consensus 326 -nhMtC~-Cg 333 (334)
||+.|+ |.
T Consensus 450 d~HllCk~Ch 459 (468)
T KOG1701|consen 450 DGHLLCKTCH 459 (468)
T ss_pred cCceeechhh
Confidence 799995 73
No 220
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=34.08 E-value=22 Score=32.01 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=4.5
Q ss_pred ccccCCCCce
Q 019929 309 WKRCPNCRYY 318 (334)
Q Consensus 309 ~k~CP~C~~~ 318 (334)
...||.|+..
T Consensus 35 v~~C~~Cg~~ 44 (236)
T PF04981_consen 35 VTICPKCGRY 44 (236)
T ss_pred ceECCCCCCE
Confidence 3444444443
No 221
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=33.92 E-value=22 Score=28.11 Aligned_cols=22 Identities=36% Similarity=0.973 Sum_probs=13.4
Q ss_pred cccCCcccccc--------ccccCccCCCC
Q 019929 258 ESECPNCRRLF--------CAQCQVPWHSG 279 (334)
Q Consensus 258 ~~~C~~C~~~f--------C~~C~~~~H~~ 279 (334)
.+.||+|++.+ |..|+.+.+-.
T Consensus 69 ~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVDACMHCKEPLTLD 98 (114)
T ss_pred eeECCCCCChHhhhchhhccCcCCCcCccC
Confidence 35555665543 78888776553
No 222
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=33.69 E-value=27 Score=30.32 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=18.0
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-.|++|+...++ .=+.|+|+ ||+
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 589999998888 34778885 885
No 223
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.40 E-value=31 Score=25.05 Aligned_cols=58 Identities=26% Similarity=0.557 Sum_probs=34.6
Q ss_pred ccccccccccCCceeEecCC--CCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhccCChHHHHHHH
Q 019929 151 VCEICAEQKTVHKSFHIKGC--SHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRDILPQDVFDRWG 223 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~~~y~ 223 (334)
.|..|-.++++...-.+ -| .|.||.+|...-+. =.|| .|+..+.-.- +-+...+.+|-
T Consensus 7 nCECCDrDLpp~s~dA~-ICtfEcTFCadCae~~l~---------g~CP--nCGGelv~RP---~RPaa~L~r~P 66 (84)
T COG3813 7 NCECCDRDLPPDSTDAR-ICTFECTFCADCAENRLH---------GLCP--NCGGELVARP---IRPAAKLARYP 66 (84)
T ss_pred CCcccCCCCCCCCCcee-EEEEeeehhHhHHHHhhc---------CcCC--CCCchhhcCc---CChHHHHhhCc
Confidence 47778777765432222 34 47899999976653 2689 6877654332 23344455543
No 224
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.32 E-value=66 Score=29.40 Aligned_cols=55 Identities=16% Similarity=0.453 Sum_probs=38.3
Q ss_pred ccccccccccccccCCce--eEecCCC-----CcccHHHHHHHHHhhhhC-CeeeeecCCCcCCCC
Q 019929 147 YGPFVCEICAEQKTVHKS--FHIKGCS-----HAYCTDCMVKYVAAKLEE-NITAIRCPVVDCRGL 204 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~--~~~~~C~-----H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~ 204 (334)
..+-.|=|||..-..... +. -+|. |.....|+..|+..+-.. ....+.|| .|...
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV-~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~--QCqTE 80 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWV-HPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCP--QCQTE 80 (293)
T ss_pred ccceeEEEEeccCcccchhhhc-ccccccCccHHHHHHHHHHHHhHHhcCCCCceeech--hhcch
Confidence 456789999976543221 22 3664 679999999999877553 35789999 58754
No 225
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.24 E-value=44 Score=25.43 Aligned_cols=12 Identities=17% Similarity=0.041 Sum_probs=6.1
Q ss_pred CCchhhhhccCC
Q 019929 204 LLEPEYCRDILP 215 (334)
Q Consensus 204 ~l~~~~i~~ll~ 215 (334)
+++...+..+++
T Consensus 18 plt~~ei~~~~~ 29 (97)
T COG3357 18 PLTVAEIFELLN 29 (97)
T ss_pred cchHHHHHHHHc
Confidence 344455555554
No 226
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.24 E-value=33 Score=29.58 Aligned_cols=30 Identities=27% Similarity=0.696 Sum_probs=18.7
Q ss_pred CcccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 235 QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 235 ~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
..+.|| .|..-+.....- ...+.||.||..
T Consensus 116 ~~Y~Cp--~C~~rytf~eA~-~~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCP--NCHIRFTFDEAM-EYGFRCPQCGEM 145 (178)
T ss_pred CEEECC--CCCcEEeHHHHh-hcCCcCCCCCCC
Confidence 345798 688766654322 234888887754
No 227
>PRK11827 hypothetical protein; Provisional
Probab=32.28 E-value=34 Score=23.97 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=18.8
Q ss_pred ccccCCCCceeeeccCCCceEee-cC
Q 019929 309 WKRCPNCRYYVEKKDGCMYMKCR-SV 333 (334)
Q Consensus 309 ~k~CP~C~~~IeK~~GCnhMtC~-Cg 333 (334)
+-.||.|+...+-..+=+...|+ ||
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~ 33 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDN 33 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccC
Confidence 35899999988876655678885 65
No 228
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=31.75 E-value=30 Score=23.27 Aligned_cols=36 Identities=19% Similarity=0.611 Sum_probs=24.7
Q ss_pred cccccccccccCCc-eeEecCCCCcccHHHHHHHHHh
Q 019929 150 FVCEICAEQKTVHK-SFHIKGCSHAYCTDCMVKYVAA 185 (334)
Q Consensus 150 ~~C~IC~e~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~ 185 (334)
..|.+|-..|.... ......||+.||..|+......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 35888876665321 2334589999999999877543
No 229
>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=31.57 E-value=20 Score=29.22 Aligned_cols=21 Identities=38% Similarity=0.896 Sum_probs=11.3
Q ss_pred CccccCC--CCceeeeccCCCceEee--cCC
Q 019929 308 KWKRCPN--CRYYVEKKDGCMYMKCR--SVF 334 (334)
Q Consensus 308 ~~k~CP~--C~~~IeK~~GCnhMtC~--Cg~ 334 (334)
..|.||+ |.-.++ +|-|+ |||
T Consensus 81 q~k~Cpn~~C~g~L~------~~pCrGh~GY 105 (143)
T PF03615_consen 81 QGKPCPNRNCKGRLE------LIPCRGHCGY 105 (143)
T ss_dssp HHSB-SS--S--BEE------EE---TBTTB
T ss_pred cCCCCCccccCCcee------EEeccCcCCC
Confidence 3489999 998775 67775 776
No 230
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.40 E-value=70 Score=26.20 Aligned_cols=14 Identities=14% Similarity=0.349 Sum_probs=10.2
Q ss_pred cccCCCCCCCceEEcC
Q 019929 236 KFYCPFKDCSAMLIDD 251 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~ 251 (334)
..+|+ +|+..+...
T Consensus 70 ~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCR--NCGNEWSLK 83 (135)
T ss_pred EEECC--CCCCEEecc
Confidence 35899 999776654
No 231
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=31.36 E-value=42 Score=22.99 Aligned_cols=30 Identities=23% Similarity=0.555 Sum_probs=15.3
Q ss_pred CcccCCCCCCCce----EEcCCccccccccCCcccc
Q 019929 235 QKFYCPFKDCSAM----LIDDGEEVIQESECPNCRR 266 (334)
Q Consensus 235 ~~~~CP~p~C~~~----~~~~~~~~~~~~~C~~C~~ 266 (334)
.++.|| -|++- +..+..-.....+||+|.+
T Consensus 3 ~Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 3 EWILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred eEEECC--CCCCccceeeecCceeccccccCCCCCc
Confidence 345788 77742 2223222333466776654
No 232
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=30.31 E-value=13 Score=38.64 Aligned_cols=56 Identities=23% Similarity=0.494 Sum_probs=39.9
Q ss_pred cccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc
Q 019929 148 GPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD 212 (334)
Q Consensus 148 ~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 212 (334)
...+|+||+..+... +++.|.|.||..||..-+...-. ...|| -|+..++...++.
T Consensus 20 k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~----~~~~~--lc~~~~eK~s~~E 75 (684)
T KOG4362|consen 20 KILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG----PKQCA--LCKSDIEKRSLRE 75 (684)
T ss_pred hhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc----cccch--hhhhhhhhhhccc
Confidence 368899999977533 45799999999999887765422 56778 4776665544443
No 233
>PLN02189 cellulose synthase
Probab=29.94 E-value=39 Score=36.98 Aligned_cols=60 Identities=18% Similarity=0.437 Sum_probs=41.3
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRY 317 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~ 317 (334)
.|. -|+..+-.+. +....+-|..|++..|..|.+ |. .+.+.+.||.|+.
T Consensus 36 ~C~--iCgd~vg~~~-~g~~fvaC~~C~fpvCr~Cye----------ye------------------r~eg~q~CpqCkt 84 (1040)
T PLN02189 36 VCE--ICGDEIGLTV-DGDLFVACNECGFPVCRPCYE----------YE------------------RREGTQNCPQCKT 84 (1040)
T ss_pred ccc--ccccccCcCC-CCCEEEeeccCCCccccchhh----------hh------------------hhcCCccCcccCC
Confidence 566 6665544332 233568999999999997743 22 1456789999999
Q ss_pred eeeeccCCCce
Q 019929 318 YVEKKDGCMYM 328 (334)
Q Consensus 318 ~IeK~~GCnhM 328 (334)
...+--|++.+
T Consensus 85 ~Y~r~kgs~~v 95 (1040)
T PLN02189 85 RYKRLKGSPRV 95 (1040)
T ss_pred chhhccCCCCc
Confidence 88877777654
No 234
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=29.76 E-value=46 Score=28.11 Aligned_cols=51 Identities=18% Similarity=0.445 Sum_probs=35.4
Q ss_pred ccccccccccccccCCceeEecCCC--C---cccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchh
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCS--H---AYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPE 208 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 208 (334)
.....|-||+++... . . .+|. . ....+|+..|+... ....|+ .|...+...
T Consensus 6 ~~~~~CRIC~~~~~~-~-~--~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Ce--iC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDV-V-T--NYCNCKNENKIVHKECLEEWINTS-----KNKSCK--ICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCC-c-c--CCcccCCCchHHHHHHHHHHHhcC-----CCCccc--ccCCeEEEE
Confidence 346789999987542 1 2 2454 3 57999999999853 356899 688777654
No 235
>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=29.56 E-value=30 Score=27.20 Aligned_cols=26 Identities=23% Similarity=0.634 Sum_probs=15.2
Q ss_pred cCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
.|| .|+.-+...... .+.||.|++.|
T Consensus 4 ~CP--~C~seytY~dg~---~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCP--KCNSEYTYHDGT---QLICPSCLYEW 29 (109)
T ss_pred cCC--cCCCcceEecCC---eeECccccccc
Confidence 477 777655554332 36777776543
No 236
>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=29.25 E-value=17 Score=24.50 Aligned_cols=29 Identities=31% Similarity=0.850 Sum_probs=16.8
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+.|+ .|+..+........-.+.||.|++.
T Consensus 5 iRC~--~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCG--HCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eecc--chhHHHhhhcCccEEEEECCCCCcc
Confidence 4566 7776655532222345777777664
No 237
>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=28.97 E-value=23 Score=24.73 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=11.7
Q ss_pred ccccCCCCceeeec
Q 019929 309 WKRCPNCRYYVEKK 322 (334)
Q Consensus 309 ~k~CP~C~~~IeK~ 322 (334)
-|.||.|+.+|.-+
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 37899999999864
No 238
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.81 E-value=32 Score=28.08 Aligned_cols=24 Identities=33% Similarity=0.736 Sum_probs=15.1
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRR 266 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~ 266 (334)
.+|| .|+..++..++ .++||.|++
T Consensus 29 ~hCp--~Cg~PLF~KdG----~v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFRKDG----EVFCPVCGY 52 (131)
T ss_pred hhCc--ccCCcceeeCC----eEECCCCCc
Confidence 4899 78876655222 267777764
No 239
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.45 E-value=39 Score=31.28 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=21.0
Q ss_pred cccCCCCceeee--ccCCCceEee-cC
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
++|+.|+.+|+| .+|=+-..|+ |.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 799999999997 7888888885 75
No 240
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=28.33 E-value=26 Score=29.66 Aligned_cols=19 Identities=21% Similarity=0.480 Sum_probs=13.9
Q ss_pred HHHHHHHhCCccccCCCCc
Q 019929 299 LLMKVAQKEKWKRCPNCRY 317 (334)
Q Consensus 299 ~~~~~~~~~~~k~CP~C~~ 317 (334)
.+.++..+...+.|++|+.
T Consensus 141 ~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 141 VFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred HHHHHhCChhhccCCccCC
Confidence 4555566677799999984
No 241
>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 TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.94 E-value=25 Score=27.96 Aligned_cols=40 Identities=23% Similarity=0.580 Sum_probs=26.4
Q ss_pred ccCCCCCCCceEEcCC------ccccccccCCccccccccccCccCCC
Q 019929 237 FYCPFKDCSAMLIDDG------EEVIQESECPNCRRLFCAQCQVPWHS 278 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~------~~~~~~~~C~~C~~~fC~~C~~~~H~ 278 (334)
..|- +|+..+.... ........|+.|+..||..|-.-+|.
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 3576 7877554321 11233578999999999999775554
No 243
>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=27.81 E-value=33 Score=31.19 Aligned_cols=95 Identities=21% Similarity=0.534 Sum_probs=57.6
Q ss_pred ccccccccccccC-----CceeEecCCCCc-ccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCchhhhhc-cCChHHHHH
Q 019929 149 PFVCEICAEQKTV-----HKSFHIKGCSHA-YCTDCMVKYVAAKLEENITAIRCPVVDCRGLLEPEYCRD-ILPQDVFDR 221 (334)
Q Consensus 149 ~~~C~IC~e~~~~-----~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-ll~~~~~~~ 221 (334)
...|..|-|-.+. .+.+..-+|... .|+. ....|.||-+.|+..|....... -+.+...
T Consensus 85 VVkC~~CnEATPIr~aPpGKKYVRCPCNCLLICk~------------sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~-- 150 (256)
T PF09788_consen 85 VVKCSVCNEATPIRNAPPGKKYVRCPCNCLLICKS------------SSQRIACPRPNCKRIINLGPSHQGPVTPPVP-- 150 (256)
T ss_pred eEECCCCCccccccCCCCCCeeEecCCceEEEeec------------ccccccCCCCCCcceEEeCCccCCCCCCCCC--
Confidence 3568888876532 334555577765 6652 23578999999999988765421 1111100
Q ss_pred HHHHHHHhhcCCCCcccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 222 WGAALCEAVIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 222 y~~~~~~~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.....-++-|. .|...+..+.......++||+|.+.
T Consensus 151 --------~~p~~~rv~Cg--hC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 151 --------TQPGSCRVICG--HCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred --------CCCCceeEECC--CCCCcEeccCCCCCccccCCCCcee
Confidence 00122346898 8998887775443456899988654
No 244
>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=27.75 E-value=37 Score=34.29 Aligned_cols=25 Identities=20% Similarity=0.498 Sum_probs=14.7
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|..+..--..=|.+.|. |||
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcC
Confidence 3677777755532233467774 775
No 245
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.73 E-value=30 Score=32.40 Aligned_cols=33 Identities=18% Similarity=0.472 Sum_probs=21.8
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHH
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYV 183 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~ 183 (334)
...|.-|--.+. -.-.+.+|.|.||.+|.+..-
T Consensus 90 VHfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~~~ 122 (389)
T KOG2932|consen 90 VHFCDRCDFPIA--IYGRMIPCKHVFCLECARSDS 122 (389)
T ss_pred eEeecccCCcce--eeecccccchhhhhhhhhcCc
Confidence 466887843322 112356999999999987643
No 246
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=27.64 E-value=61 Score=23.01 Aligned_cols=32 Identities=19% Similarity=0.478 Sum_probs=19.7
Q ss_pred CcccCCCCCCCceEEcCCccccccccCCccccc
Q 019929 235 QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 235 ~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.+.-||..+|..+.+.... ....+.|..|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~-g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAIS-GYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecC-ceEEEEcCCCCcC
Confidence 4568997777766655542 2334677777664
No 247
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=27.57 E-value=27 Score=30.12 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=16.6
Q ss_pred HHHHHHHhCCccccCCCCceeee
Q 019929 299 LLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 299 ~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
.+.++..+...+.|++|+..-..
T Consensus 147 ~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 147 VFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred HHHHHhcCHhhccCCcCCcccCc
Confidence 45555666777999999986543
No 248
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=27.47 E-value=42 Score=30.95 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=18.0
Q ss_pred cccCCCCceeee--ccCCCceEee-cC
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
++||.|+..|+| .+|=.-..|+ |.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 789999999997 5665556663 53
No 249
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=27.27 E-value=47 Score=25.93 Aligned_cols=24 Identities=25% Similarity=0.819 Sum_probs=20.2
Q ss_pred cCCCCcccHHHHHHHHHhhhhCCeeeeecCC
Q 019929 168 KGCSHAYCTDCMVKYVAAKLEENITAIRCPV 198 (334)
Q Consensus 168 ~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 198 (334)
-.|.|.|..-|+..|++++ -.||.
T Consensus 79 G~CNHaFH~hCisrWlktr-------~vCPL 102 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR-------NVCPL 102 (114)
T ss_pred eecchHHHHHHHHHHHhhc-------CcCCC
Confidence 3699999999999999873 37884
No 250
>PRK10220 hypothetical protein; Provisional
Probab=26.94 E-value=42 Score=26.45 Aligned_cols=25 Identities=24% Similarity=0.674 Sum_probs=14.8
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
.|| .|+.-+...... .+.||.|++.
T Consensus 5 ~CP--~C~seytY~d~~---~~vCpeC~hE 29 (111)
T PRK10220 5 HCP--KCNSEYTYEDNG---MYICPECAHE 29 (111)
T ss_pred cCC--CCCCcceEcCCC---eEECCcccCc
Confidence 577 777655554332 3677776654
No 251
>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=26.86 E-value=35 Score=26.31 Aligned_cols=24 Identities=25% Similarity=0.862 Sum_probs=16.9
Q ss_pred cCCCCCCCceEEcCCccccccccCCccccc
Q 019929 238 YCPFKDCSAMLIDDGEEVIQESECPNCRRL 267 (334)
Q Consensus 238 ~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~ 267 (334)
+|| .|+.++.+.. ..+.|+.|++.
T Consensus 2 fC~--~Cg~~l~~~~----~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCP--KCGSLMTPKN----GVYVCPSCGYE 25 (104)
T ss_pred CCc--ccCcccccCC----CeEECcCCCCc
Confidence 688 9999886532 24778777765
No 252
>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=26.51 E-value=45 Score=30.76 Aligned_cols=23 Identities=26% Similarity=0.437 Sum_probs=18.1
Q ss_pred cccCCCCceeee--ccCCCceEee-c
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKCR-S 332 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC~-C 332 (334)
++||.|+..|+| .+|=.-..|+ |
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCC
Confidence 699999999997 5676666664 5
No 253
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.11 E-value=45 Score=30.75 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=18.7
Q ss_pred ccccCCCCceeee--ccCCCceEee-cC
Q 019929 309 WKRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 309 ~k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
-++||+|+..|++ .+|=.-..|+ |.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 3799999999997 6676666663 53
No 254
>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=26.07 E-value=33 Score=25.55 Aligned_cols=27 Identities=33% Similarity=0.615 Sum_probs=15.0
Q ss_pred CccccCCCC------ceeeeccCCCceEee-cCC
Q 019929 308 KWKRCPNCR------YYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 308 ~~k~CP~C~------~~IeK~~GCnhMtC~-Cg~ 334 (334)
..-.||.|+ +.|.|..|=-+++|. ||.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~ 54 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGE 54 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCC
Confidence 446999999 245567788889995 874
No 255
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=25.92 E-value=59 Score=26.35 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=25.2
Q ss_pred HHHHHHHhCCccccCCCCc---eeeeccCCCceEee-cCC
Q 019929 299 LLMKVAQKEKWKRCPNCRY---YVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 299 ~~~~~~~~~~~k~CP~C~~---~IeK~~GCnhMtC~-Cg~ 334 (334)
.+..++ ...-.||.|+. .+.|.++=..|.|. ||.
T Consensus 85 ~L~~fI--~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 85 LLDKFI--KEYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HHHHHH--CHHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HHHHHH--HHEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 344444 34579999998 46678999999996 985
No 256
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.91 E-value=45 Score=30.76 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=18.7
Q ss_pred ccccCCCCceeee--ccCCCceEee-cC
Q 019929 309 WKRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 309 ~k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
-++||.|+..|+| .+|=.-..|+ |.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 3799999999987 6676666664 63
No 257
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=25.52 E-value=40 Score=22.05 Aligned_cols=34 Identities=15% Similarity=0.458 Sum_probs=24.3
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHHHH
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVA 184 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 184 (334)
.|.||.......+++.-..|+..|...|+.-...
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 3778887656666777778888888888765443
No 258
>PF14353 CpXC: CpXC protein
Probab=25.34 E-value=47 Score=26.66 Aligned_cols=44 Identities=25% Similarity=0.539 Sum_probs=24.5
Q ss_pred eecCCCcCCCCCchhhhhcc---CChHHHHHHHHHHHHhhcC-CCCcccCCCCCCCceEE
Q 019929 194 IRCPVVDCRGLLEPEYCRDI---LPQDVFDRWGAALCEAVIP-GAQKFYCPFKDCSAMLI 249 (334)
Q Consensus 194 i~CP~~~C~~~l~~~~i~~l---l~~~~~~~y~~~~~~~~~~-~~~~~~CP~p~C~~~~~ 249 (334)
|.|| .|+..+..+....+ .++++.++. +. .-..+.|| .|+..+.
T Consensus 2 itCP--~C~~~~~~~v~~~I~~~~~p~l~e~i--------l~g~l~~~~CP--~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCP--HCGHEFEFEVWTSINADEDPELKEKI--------LDGSLFSFTCP--SCGHKFR 49 (128)
T ss_pred cCCC--CCCCeeEEEEEeEEcCcCCHHHHHHH--------HcCCcCEEECC--CCCCcee
Confidence 6899 69888877654433 334444432 21 12234787 7775443
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=25.27 E-value=98 Score=24.57 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=23.2
Q ss_pred cccCCCCCCCceEEcCCccccccccCCccccccccccCcc
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVP 275 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 275 (334)
...|. .|...+..-. .....|..|+..+|..|+..
T Consensus 54 ~~~C~--~C~~~fg~l~---~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCA--RCGKPFGFLF---NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-T--TTS-BCSCTS---TTCEEETTTTEEEETTSEEE
T ss_pred Ccchh--hhCCcccccC---CCCCcCCcCCccccCccCCc
Confidence 35787 7876432221 12378999999999999986
No 260
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=25.23 E-value=36 Score=28.42 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=7.8
Q ss_pred ccccCCCCce
Q 019929 309 WKRCPNCRYY 318 (334)
Q Consensus 309 ~k~CP~C~~~ 318 (334)
.-+||+|+.-
T Consensus 130 l~~Cp~C~~~ 139 (146)
T PF07295_consen 130 LPPCPKCGHT 139 (146)
T ss_pred CCCCCCCCCC
Confidence 4799999863
No 261
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=25.19 E-value=1e+02 Score=28.23 Aligned_cols=48 Identities=25% Similarity=0.490 Sum_probs=34.2
Q ss_pred ccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCC
Q 019929 149 PFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRG 203 (334)
Q Consensus 149 ~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 203 (334)
...|||=+-.+. .++....|||.|=++=+..++.. ...+.||..+|..
T Consensus 176 s~rdPis~~~I~--nPviSkkC~HvydrDsI~~~l~~-----~~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIV--NPVISKKCGHVYDRDSIMQILCD-----EITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhh--chhhhcCcCcchhhhhHHHHhcc-----CceeecccccCCc
Confidence 567887654443 33333589999999888777643 3578999999984
No 262
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.10 E-value=48 Score=23.69 Aligned_cols=31 Identities=19% Similarity=0.426 Sum_probs=20.0
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCA 270 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 270 (334)
+.|| +|.+.-..-.. ....+.|..||...+.
T Consensus 20 VkCp--dC~N~q~vFsh-ast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP--DCGNEQVVFSH-ASTVVTCLICGTTLAE 50 (67)
T ss_pred EECC--CCCCEEEEecc-CceEEEecccccEEEe
Confidence 4799 99875332111 2345899999987764
No 263
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=25.06 E-value=23 Score=34.29 Aligned_cols=36 Identities=22% Similarity=0.460 Sum_probs=27.5
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYV 183 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~ 183 (334)
....+|+|||-.++....... .|...+|..|+..+-
T Consensus 72 rr~~ecpicflyyps~~n~~r-cC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNLVR-CCSETICGECFAPFG 107 (482)
T ss_pred cccccCceeeeecccccchhh-hhccchhhhheeccc
Confidence 356899999988875443443 799999999998753
No 264
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.87 E-value=48 Score=30.74 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=19.0
Q ss_pred cccCCCCceeee--ccCCCceEee-cC
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
++||.|+..|+| .+|=.-..|+ |.
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 799999999987 6776666674 64
No 265
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=24.74 E-value=55 Score=21.58 Aligned_cols=35 Identities=29% Similarity=0.707 Sum_probs=25.9
Q ss_pred ccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhC
Q 019929 151 VCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEE 189 (334)
Q Consensus 151 ~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 189 (334)
.|.||-.... +.+.+ .++.+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~--~GI~I--~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKE--EGIHI--YGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCC--CCEEE--ECeEehHHHHHHhccCCCCC
Confidence 3888887654 34444 69999999999998876654
No 266
>PRK10445 endonuclease VIII; Provisional
Probab=24.55 E-value=51 Score=30.27 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=18.8
Q ss_pred cccCCCCceeee--ccCCCceEee-cC
Q 019929 310 KRCPNCRYYVEK--KDGCMYMKCR-SV 333 (334)
Q Consensus 310 k~CP~C~~~IeK--~~GCnhMtC~-Cg 333 (334)
++||.|+..|++ .+|=.-..|+ |.
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 799999999997 6776666674 63
No 267
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=24.37 E-value=34 Score=21.20 Aligned_cols=31 Identities=23% Similarity=0.629 Sum_probs=15.8
Q ss_pred ccHHHHHHHHHhhhhC-CeeeeecCCCcCCCCCc
Q 019929 174 YCTDCMVKYVAAKLEE-NITAIRCPVVDCRGLLE 206 (334)
Q Consensus 174 fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~l~ 206 (334)
+|.+|++.|....-.. ....+.|+ .|+-.+.
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~--~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCT--NCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BT--TCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCC--CCCCCEE
Confidence 5889999886543211 34678898 5775544
No 268
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.28 E-value=27 Score=33.42 Aligned_cols=39 Identities=31% Similarity=0.728 Sum_probs=25.9
Q ss_pred CCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeee
Q 019929 261 CPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEK 321 (334)
Q Consensus 261 C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK 321 (334)
=|.|.+.||.+|...|+.-.. ......+-||-|++.+..
T Consensus 184 lpnC~H~~Cl~Cir~wr~~~q----------------------~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 184 LPNCNHSFCLNCIRKWRQATQ----------------------FESKTSKSCPFCRVPSSF 222 (344)
T ss_pred CCCcchhhhhcHhHhhhhhhc----------------------cccccccCCCcccCcccc
Confidence 368999999999876643210 013456888888876643
No 269
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.21 E-value=39 Score=19.02 Aligned_cols=10 Identities=50% Similarity=1.162 Sum_probs=7.4
Q ss_pred ccCCcccccc
Q 019929 259 SECPNCRRLF 268 (334)
Q Consensus 259 ~~C~~C~~~f 268 (334)
+.|+.||..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5678887776
No 270
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.17 E-value=68 Score=29.75 Aligned_cols=28 Identities=14% Similarity=0.279 Sum_probs=22.3
Q ss_pred CCccccCCCCceeeeccCCCceEee-cCC
Q 019929 307 EKWKRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 307 ~~~k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
...+-||+|+...+-..|=-.|.|. ||+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCC
Confidence 4459999999999888877777774 774
No 271
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=24.07 E-value=37 Score=23.55 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=8.5
Q ss_pred ccccCCCCceeeecc
Q 019929 309 WKRCPNCRYYVEKKD 323 (334)
Q Consensus 309 ~k~CP~C~~~IeK~~ 323 (334)
+..||.|+..++-..
T Consensus 2 ~v~CP~C~k~~~~~~ 16 (57)
T PF03884_consen 2 TVKCPICGKPVEWSP 16 (57)
T ss_dssp EEE-TTT--EEE-SS
T ss_pred cccCCCCCCeecccC
Confidence 578999999988643
No 272
>PLN00209 ribosomal protein S27; Provisional
Probab=23.65 E-value=83 Score=23.72 Aligned_cols=32 Identities=16% Similarity=0.445 Sum_probs=20.5
Q ss_pred ccCCCCCCCceEEcCCccccccccCCccccccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQ 271 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 271 (334)
+.|| +|...-+.-. .....+.|..|+...|.-
T Consensus 37 VkCp--~C~n~q~VFS-hA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 37 VKCQ--GCFNITTVFS-HSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred EECC--CCCCeeEEEe-cCceEEEccccCCEeecc
Confidence 4799 9987432211 123458899999888753
No 273
>PLN02400 cellulose synthase
Probab=23.56 E-value=44 Score=36.76 Aligned_cols=45 Identities=20% Similarity=0.541 Sum_probs=33.8
Q ss_pred cccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeeccCCCce
Q 019929 256 IQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKKDGCMYM 328 (334)
Q Consensus 256 ~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~~GCnhM 328 (334)
...+-|..|+...|..|.+ |.+ +.+.+-||.|++...+--|+..+
T Consensus 53 e~FVAC~eCaFPVCRpCYE----------YER------------------keGnq~CPQCkTrYkR~KgsprV 97 (1085)
T PLN02400 53 DVFVACNECAFPVCRPCYE----------YER------------------KDGTQCCPQCKTRYRRHKGSPRV 97 (1085)
T ss_pred CEEEEEccCCCccccchhh----------eec------------------ccCCccCcccCCccccccCCCCC
Confidence 3568999999999987753 221 46678999999988877777654
No 274
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=23.28 E-value=53 Score=26.75 Aligned_cols=16 Identities=25% Similarity=0.484 Sum_probs=11.8
Q ss_pred cccCCCCceeeeccCC
Q 019929 310 KRCPNCRYYVEKKDGC 325 (334)
Q Consensus 310 k~CP~C~~~IeK~~GC 325 (334)
|.||+|+.-|--.+++
T Consensus 111 K~C~~C~tGiYS~e~~ 126 (128)
T PF11682_consen 111 KYCPKCGTGIYSIEVT 126 (128)
T ss_pred EecCCCCCcccceecc
Confidence 8999999877654443
No 275
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.20 E-value=40 Score=32.21 Aligned_cols=44 Identities=25% Similarity=0.647 Sum_probs=28.2
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCC
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLL 205 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 205 (334)
.....|.||.++.. + +...+|||..| |..-+-. ...|| -|...+
T Consensus 303 ~~p~lcVVcl~e~~--~-~~fvpcGh~cc--ct~cs~~--------l~~CP--vCR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPK--S-AVFVPCGHVCC--CTLCSKH--------LPQCP--VCRQRI 346 (355)
T ss_pred CCCCceEEecCCcc--c-eeeecCCcEEE--chHHHhh--------CCCCc--hhHHHH
Confidence 44678999998754 3 44569999976 5543321 23599 475543
No 276
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=22.81 E-value=31 Score=26.72 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=22.2
Q ss_pred ccccccccccccccCCceeEecCCCCcccHHH
Q 019929 147 YGPFVCEICAEQKTVHKSFHIKGCSHAYCTDC 178 (334)
Q Consensus 147 ~~~~~C~IC~e~~~~~~~~~~~~C~H~fC~~C 178 (334)
..+|+|.-||=....++... ..=|+.+|++|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 45899999997655544333 34588899988
No 277
>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=22.12 E-value=62 Score=26.30 Aligned_cols=27 Identities=19% Similarity=0.344 Sum_probs=15.9
Q ss_pred ccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 237 FYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 237 ~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
+.|| .|+.-+.--. ...+.||+||..|
T Consensus 10 r~Cp--~cg~kFYDLn---k~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICP--NTGSKFYDLN---RRPAVSPYTGEQF 36 (129)
T ss_pred ccCC--CcCccccccC---CCCccCCCcCCcc
Confidence 4688 7776543211 1337788887764
No 278
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.91 E-value=43 Score=21.40 Aligned_cols=25 Identities=28% Similarity=0.610 Sum_probs=13.9
Q ss_pred cccccccccccCCceeEecCC----CCcccHHH
Q 019929 150 FVCEICAEQKTVHKSFHIKGC----SHAYCTDC 178 (334)
Q Consensus 150 ~~C~IC~e~~~~~~~~~~~~C----~H~fC~~C 178 (334)
..||+|-.. +.|.+..= ++.||+.|
T Consensus 4 ~pCP~CGG~----DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGK----DRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-T----TTEEEETT----S-EEETTT
T ss_pred CCCCCCcCc----cccccCcCcccCCCEECCCC
Confidence 459999653 44553344 89999988
No 280
>PRK11032 hypothetical protein; Provisional
Probab=21.86 E-value=45 Score=28.26 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=8.5
Q ss_pred CCccccCCCCce
Q 019929 307 EKWKRCPNCRYY 318 (334)
Q Consensus 307 ~~~k~CP~C~~~ 318 (334)
...-+||+|+.-
T Consensus 140 ~~i~pCp~C~~~ 151 (160)
T PRK11032 140 EVLPLCPKCGHD 151 (160)
T ss_pred CcCCCCCCCCCC
Confidence 344799999863
No 281
>PRK02935 hypothetical protein; Provisional
Probab=21.79 E-value=53 Score=25.72 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=7.0
Q ss_pred cccccCccCCC
Q 019929 268 FCAQCQVPWHS 278 (334)
Q Consensus 268 fC~~C~~~~H~ 278 (334)
.|..|+.|-+-
T Consensus 88 ~CM~C~~PLTL 98 (110)
T PRK02935 88 ACMHCNQPLTL 98 (110)
T ss_pred ecCcCCCcCCc
Confidence 46777776544
No 282
>PRK06386 replication factor A; Reviewed
Probab=21.70 E-value=40 Score=32.53 Aligned_cols=14 Identities=21% Similarity=0.719 Sum_probs=12.2
Q ss_pred CccccCCCCceeee
Q 019929 308 KWKRCPNCRYYVEK 321 (334)
Q Consensus 308 ~~k~CP~C~~~IeK 321 (334)
-.++||.|+..+++
T Consensus 235 li~rCP~C~R~l~~ 248 (358)
T PRK06386 235 IFTKCSVCNKIIED 248 (358)
T ss_pred eEecCcCCCeEccC
Confidence 45899999999996
No 283
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=21.61 E-value=29 Score=31.21 Aligned_cols=118 Identities=21% Similarity=0.463 Sum_probs=59.0
Q ss_pred ccccc--cccccccCCceeEecCCCCcccHHHHHHHHHhhhh-------CCeeeeecCCCcCCCCCchhhhhccCChHHH
Q 019929 149 PFVCE--ICAEQKTVHKSFHIKGCSHAYCTDCMVKYVAAKLE-------ENITAIRCPVVDCRGLLEPEYCRDILPQDVF 219 (334)
Q Consensus 149 ~~~C~--IC~e~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~-------~~~~~i~CP~~~C~~~l~~~~i~~ll~~~~~ 219 (334)
...|. .|-.. ..-+|..-.|++.||.+ |..-.-. .++....|| .|..+++.. ..-.....+
T Consensus 8 GkHCs~~~Ckql--DFLPf~Cd~C~~~FC~e----Hrsye~H~Cp~~~~~~~~v~icp--~cs~pv~~~--~de~~~~~v 77 (250)
T KOG3183|consen 8 GKHCSVPYCKQL--DFLPFKCDGCSGIFCLE----HRSYESHHCPKGLRIDVQVPICP--LCSKPVPTK--KDEAPDKVV 77 (250)
T ss_pred ccccCcchhhhc--cccceeeCCccchhhhc----cchHhhcCCCcccccceeecccC--CCCCCCCCC--CCcchhhhh
Confidence 34566 56432 11235667899999975 2222111 123445788 577766654 111111112
Q ss_pred HHHHHHHHHh----hcCCCCcccCCCCCCCceEEcCCccccccccCCccccccccccCccCCCCCCch
Q 019929 220 DRWGAALCEA----VIPGAQKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQVPWHSGINCV 283 (334)
Q Consensus 220 ~~y~~~~~~~----~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~tC~ 283 (334)
..+...-.+. .........||.|.|...... .+.+.|..|+..||.+-+.+ .+++|.
T Consensus 78 ~~h~~~dC~~~~~~~~~k~~t~kc~~~~c~k~~~~-----~~~~~c~~c~~~~c~khr~~--~dhsc~ 138 (250)
T KOG3183|consen 78 EPHISNDCDRHPEQKKRKVFTNKCPVPRCKKTLTL-----ANKITCSKCGRNFCLKHRHP--LDHSCN 138 (250)
T ss_pred chhhccccccCchhhhcccccccCCchhhHHHHHH-----HHhhhhHhhcchhhhhccCC--CCchhh
Confidence 2221111111 001112236888888764332 34488999999999876543 144565
No 284
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=21.60 E-value=60 Score=30.58 Aligned_cols=11 Identities=27% Similarity=0.984 Sum_probs=8.7
Q ss_pred cccCCCCceee
Q 019929 310 KRCPNCRYYVE 320 (334)
Q Consensus 310 k~CP~C~~~Ie 320 (334)
-.|..|+.++.
T Consensus 253 e~C~~C~~YlK 263 (305)
T TIGR01562 253 ETCDSCQGYLK 263 (305)
T ss_pred eeccccccchh
Confidence 48999998764
No 285
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.54 E-value=55 Score=23.18 Aligned_cols=31 Identities=16% Similarity=0.483 Sum_probs=23.8
Q ss_pred CcccCCCCCCCceEEcCCccccccccCCccccccccccCc
Q 019929 235 QKFYCPFKDCSAMLIDDGEEVIQESECPNCRRLFCAQCQV 274 (334)
Q Consensus 235 ~~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 274 (334)
....|+.++|+.. ..+.|..|...+|+..-.
T Consensus 26 ~~~~C~~~gC~~~---------s~I~C~~Ckk~~Cf~Hfi 56 (63)
T PF04236_consen 26 VAGDCDITGCNNT---------SFIRCAYCKKSLCFNHFI 56 (63)
T ss_pred CcCcCCCCCCCCc---------CEEEccccCCccccccee
Confidence 3457888888763 337899999999998765
No 286
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=21.54 E-value=90 Score=23.24 Aligned_cols=18 Identities=22% Similarity=0.785 Sum_probs=16.4
Q ss_pred cCCCCcccHHHHHHHHHh
Q 019929 168 KGCSHAYCTDCMVKYVAA 185 (334)
Q Consensus 168 ~~C~H~fC~~Cl~~~~~~ 185 (334)
--|.|.|-..|+.+|+.+
T Consensus 52 G~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred EecchHHHHHHHHHHHhh
Confidence 369999999999999987
No 287
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.51 E-value=64 Score=23.88 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=6.6
Q ss_pred cCCCCCCCceEEcC
Q 019929 238 YCPFKDCSAMLIDD 251 (334)
Q Consensus 238 ~CP~p~C~~~~~~~ 251 (334)
-|| .|+..+...
T Consensus 3 lCP--~C~v~l~~~ 14 (88)
T COG3809 3 LCP--ICGVELVMS 14 (88)
T ss_pred ccC--cCCceeeee
Confidence 466 666555443
No 288
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.48 E-value=61 Score=35.52 Aligned_cols=45 Identities=22% Similarity=0.586 Sum_probs=33.0
Q ss_pred cccccCCccccccccccCccCCCCCCchhHHHHhhhhhhHHHHHHHHHHHhCCccccCCCCceeeeccCCCce
Q 019929 256 IQESECPNCRRLFCAQCQVPWHSGINCVEFQKLNKDEREREDILLMKVAQKEKWKRCPNCRYYVEKKDGCMYM 328 (334)
Q Consensus 256 ~~~~~C~~C~~~fC~~C~~~~H~~~tC~~~~~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~IeK~~GCnhM 328 (334)
...+-|..|+...|..|.. |. .+.+.+-||+|+....+--|++.+
T Consensus 32 e~FVAC~eC~fpvCr~cye----------ye------------------~~~g~~~cp~c~t~y~~~~~~~~~ 76 (1044)
T PLN02915 32 QPFVACHVCGFPVCKPCYE----------YE------------------RSEGNQCCPQCNTRYKRHKGCPRV 76 (1044)
T ss_pred CEEEEeccCCCccccchhh----------hh------------------hhcCCccCCccCCchhhhcCCCCc
Confidence 3568999999999987743 22 145668999999988766666544
No 289
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.05 E-value=48 Score=29.37 Aligned_cols=27 Identities=26% Similarity=0.680 Sum_probs=20.5
Q ss_pred cccccccccCCceeEecCCCCc-ccHHHHHH
Q 019929 152 CEICAEQKTVHKSFHIKGCSHA-YCTDCMVK 181 (334)
Q Consensus 152 C~IC~e~~~~~~~~~~~~C~H~-fC~~Cl~~ 181 (334)
|-.|.+. ...+.++||.|. +|..|-..
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~ 188 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES 188 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc
Confidence 8899874 234667899998 99999654
No 290
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=20.97 E-value=1.1e+02 Score=33.68 Aligned_cols=51 Identities=25% Similarity=0.707 Sum_probs=33.9
Q ss_pred cccccccccccccC---Ccee-EecCCCCcccHHHHHHHHHhhhhCCeeeeecCCCcCCCCCc
Q 019929 148 GPFVCEICAEQKTV---HKSF-HIKGCSHAYCTDCMVKYVAAKLEENITAIRCPVVDCRGLLE 206 (334)
Q Consensus 148 ~~~~C~IC~e~~~~---~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 206 (334)
....|.||-+++.. .++| ..-.|+-..|+.|. .|=. ++|. -.|| .|+....
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr---~eG~--q~CP--qCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER---KDGN--QSCP--QCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh---hcCC--ccCC--ccCCchh
Confidence 35689999998743 2344 45578888999999 4432 3443 3799 5876544
No 291
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.84 E-value=92 Score=24.70 Aligned_cols=25 Identities=28% Similarity=0.694 Sum_probs=16.3
Q ss_pred cccCCCCCCCceEEcCCccccccccCCcccc
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRR 266 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~ 266 (334)
..+|+ +|+..+..... .+.||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~~----~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECE--DCSEEVSPEID----LYRCPKCHG 94 (115)
T ss_pred EEEcc--cCCCEEecCCc----CccCcCCcC
Confidence 35898 88876655422 366888774
No 292
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.67 E-value=75 Score=19.33 Aligned_cols=29 Identities=24% Similarity=0.349 Sum_probs=15.7
Q ss_pred cccCCCCCCCceEEcCCccccccccCCcccccc
Q 019929 236 KFYCPFKDCSAMLIDDGEEVIQESECPNCRRLF 268 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~~~~~~~C~~C~~~f 268 (334)
...|+ .|+...+.... .....|+.|+..|
T Consensus 3 ~~~C~--~C~~~~i~~~~--~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNKE--DDYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEec--CCeEEcccCCcEe
Confidence 34577 68765544211 1236777777654
No 293
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=20.67 E-value=51 Score=20.12 Aligned_cols=13 Identities=38% Similarity=0.879 Sum_probs=9.6
Q ss_pred ccccCCCCceeee
Q 019929 309 WKRCPNCRYYVEK 321 (334)
Q Consensus 309 ~k~CP~C~~~IeK 321 (334)
+-.||+|+..|.-
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 4689999998864
No 294
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=20.41 E-value=46 Score=19.93 Aligned_cols=9 Identities=44% Similarity=0.980 Sum_probs=6.2
Q ss_pred ccCCCCcee
Q 019929 311 RCPNCRYYV 319 (334)
Q Consensus 311 ~CP~C~~~I 319 (334)
-||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999844
No 295
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.33 E-value=62 Score=34.03 Aligned_cols=25 Identities=16% Similarity=0.477 Sum_probs=17.7
Q ss_pred cccCCCCceeeeccCCCceEee-cCC
Q 019929 310 KRCPNCRYYVEKKDGCMYMKCR-SVF 334 (334)
Q Consensus 310 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 334 (334)
-.||+|..+..--..=+.++|. |||
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 416 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGY 416 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcC
Confidence 4799999876633333678995 986
No 296
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=20.31 E-value=1.4e+02 Score=24.74 Aligned_cols=31 Identities=26% Similarity=0.602 Sum_probs=18.9
Q ss_pred cccCCCCCCCceEEcCCcc-------------ccccccCCcccccc
Q 019929 236 KFYCPFKDCSAMLIDDGEE-------------VIQESECPNCRRLF 268 (334)
Q Consensus 236 ~~~CP~p~C~~~~~~~~~~-------------~~~~~~C~~C~~~f 268 (334)
...|+ .|+..+...... ......|+.|++.|
T Consensus 91 ~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 34899 898876543221 12356777777765
No 297
>PHA02325 hypothetical protein
Probab=20.28 E-value=53 Score=23.24 Aligned_cols=11 Identities=36% Similarity=0.733 Sum_probs=9.1
Q ss_pred CccccCCCCce
Q 019929 308 KWKRCPNCRYY 318 (334)
Q Consensus 308 ~~k~CP~C~~~ 318 (334)
.+|.||+|++.
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 46899999984
No 298
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=20.20 E-value=1.1e+02 Score=27.95 Aligned_cols=30 Identities=17% Similarity=0.402 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHhhcCCCCcccCCCCCCCce
Q 019929 216 QDVFDRWGAALCEAVIPGAQKFYCPFKDCSAM 247 (334)
Q Consensus 216 ~~~~~~y~~~~~~~~~~~~~~~~CP~p~C~~~ 247 (334)
.+-+.+|.+...+..-.....|-|. .|...
T Consensus 92 e~Nlrm~d~a~~~~ip~~drqFaC~--~Cd~~ 121 (278)
T PF15135_consen 92 EENLRMFDDAQENLIPSVDRQFACS--SCDHM 121 (278)
T ss_pred HHHHHHhhhhhhccccccceeeecc--ccchH
Confidence 3444555544332222222335666 66543
No 299
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.19 E-value=68 Score=22.41 Aligned_cols=23 Identities=4% Similarity=-0.200 Sum_probs=16.5
Q ss_pred CCccccCCCCceeeeccCCCceEeecCC
Q 019929 307 EKWKRCPNCRYYVEKKDGCMYMKCRSVF 334 (334)
Q Consensus 307 ~~~k~CP~C~~~IeK~~GCnhMtC~Cg~ 334 (334)
...-.||+|+.++. .|=.|.|||
T Consensus 25 ~~~~~c~~cg~~~~-----pH~vc~cG~ 47 (60)
T PRK01110 25 PTLSVDKTTGEYHL-----PHHVSPKGY 47 (60)
T ss_pred CceeEcCCCCceec-----cceecCCcc
Confidence 44578999998774 466677775
Done!