Query 048441
Match_columns 292
No_of_seqs 241 out of 1260
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 09:34:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048441hhsearch_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 3.2E-30 6.9E-35 241.4 8.6 151 105-257 144-346 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 2.4E-29 5.1E-34 228.5 6.3 158 106-264 183-416 (445)
3 KOG1815 Predicted E3 ubiquitin 99.9 1.2E-24 2.6E-29 208.6 2.0 180 107-289 70-309 (444)
4 KOG0006 E3 ubiquitin-protein l 99.7 3.2E-18 6.9E-23 151.2 3.5 152 105-261 219-444 (446)
5 KOG0320 Predicted E3 ubiquitin 99.0 5.4E-10 1.2E-14 92.0 7.1 57 105-171 129-185 (187)
6 smart00647 IBR In Between Ring 98.5 2.1E-07 4.5E-12 65.0 5.2 48 207-254 7-60 (64)
7 PF13639 zf-RING_2: Ring finge 98.5 5.5E-08 1.2E-12 63.0 1.6 41 109-156 2-42 (44)
8 PF13923 zf-C3HC4_2: Zinc fing 98.3 4.1E-07 8.8E-12 57.4 3.1 38 110-156 1-38 (39)
9 PF00097 zf-C3HC4: Zinc finger 98.3 3.8E-07 8.2E-12 58.0 2.9 39 110-155 1-39 (41)
10 PF13445 zf-RING_UBOX: RING-ty 98.3 6.2E-07 1.4E-11 57.7 2.9 42 110-155 1-43 (43)
11 PF01485 IBR: IBR domain; Int 98.2 3.2E-07 7E-12 64.0 0.6 39 216-254 17-60 (64)
12 PF14634 zf-RING_5: zinc-RING 98.2 1.7E-06 3.7E-11 56.0 3.2 43 109-160 1-43 (44)
13 PF15227 zf-C3HC4_4: zinc fing 98.2 5.1E-07 1.1E-11 57.9 0.7 40 110-155 1-40 (42)
14 cd00162 RING RING-finger (Real 98.1 3.2E-06 7E-11 54.0 4.0 44 109-162 1-44 (45)
15 PLN03208 E3 ubiquitin-protein 98.1 3.4E-06 7.3E-11 71.4 3.6 63 107-174 18-89 (193)
16 PF13920 zf-C3HC4_3: Zinc fing 97.9 1.5E-05 3.2E-10 53.0 3.4 46 107-164 2-48 (50)
17 PHA02929 N1R/p28-like protein; 97.8 1.6E-05 3.6E-10 69.9 4.2 49 107-164 174-227 (238)
18 KOG2164 Predicted E3 ubiquitin 97.8 1.1E-05 2.4E-10 76.9 2.1 58 107-171 186-243 (513)
19 smart00184 RING Ring finger. E 97.8 2.8E-05 6E-10 47.8 3.1 37 110-155 1-37 (39)
20 PHA02926 zinc finger-like prot 97.6 6.6E-05 1.4E-09 64.6 3.5 54 107-163 170-229 (242)
21 smart00504 Ubox Modified RING 97.5 0.00012 2.6E-09 50.7 4.2 49 108-168 2-50 (63)
22 KOG0823 Predicted E3 ubiquitin 97.5 5E-05 1.1E-09 65.6 2.4 60 106-174 46-105 (230)
23 KOG0317 Predicted E3 ubiquitin 97.4 0.00012 2.7E-09 65.1 3.6 52 105-168 237-288 (293)
24 COG5540 RING-finger-containing 97.4 0.00016 3.5E-09 64.7 3.6 52 106-165 322-373 (374)
25 TIGR00570 cdk7 CDK-activating 97.3 0.00018 3.9E-09 65.4 3.7 53 107-167 3-57 (309)
26 KOG0978 E3 ubiquitin ligase in 97.1 0.00016 3.4E-09 72.2 0.7 55 106-171 642-696 (698)
27 TIGR00599 rad18 DNA repair pro 97.0 0.00041 8.9E-09 65.5 2.9 47 107-165 26-72 (397)
28 KOG4628 Predicted E3 ubiquitin 97.0 0.00056 1.2E-08 63.2 3.1 46 108-161 230-275 (348)
29 PF12678 zf-rbx1: RING-H2 zinc 96.9 0.00096 2.1E-08 48.0 3.5 42 108-156 20-71 (73)
30 KOG2177 Predicted E3 ubiquitin 96.9 0.00039 8.4E-09 62.4 1.5 43 106-160 12-54 (386)
31 smart00647 IBR In Between Ring 96.8 0.0015 3.1E-08 45.3 3.6 50 143-192 10-64 (64)
32 KOG0287 Postreplication repair 96.8 0.00064 1.4E-08 61.8 1.6 50 106-167 22-71 (442)
33 PF01485 IBR: IBR domain; Int 96.7 0.00041 8.8E-09 48.1 0.3 46 147-192 14-64 (64)
34 PF11789 zf-Nse: Zinc-finger o 96.7 0.0013 2.9E-08 44.9 2.5 47 107-160 11-57 (57)
35 COG5574 PEX10 RING-finger-cont 96.5 0.0029 6.2E-08 55.9 3.7 54 105-168 213-266 (271)
36 PF14835 zf-RING_6: zf-RING of 96.1 0.00095 2.1E-08 46.3 -1.0 48 107-167 7-54 (65)
37 KOG1428 Inhibitor of type V ad 96.0 0.0035 7.6E-08 66.3 2.3 141 106-253 3485-3685(3738)
38 KOG2879 Predicted E3 ubiquitin 95.7 0.015 3.2E-07 51.7 4.4 52 105-165 237-288 (298)
39 PF11793 FANCL_C: FANCL C-term 95.3 0.015 3.2E-07 41.5 2.6 57 107-165 2-67 (70)
40 KOG1039 Predicted E3 ubiquitin 95.0 0.02 4.4E-07 53.2 3.2 56 105-162 159-219 (344)
41 KOG1002 Nucleotide excision re 95.0 0.0085 1.9E-07 57.6 0.8 54 106-166 535-588 (791)
42 KOG0311 Predicted E3 ubiquitin 95.0 0.0032 7E-08 57.7 -2.1 49 106-164 42-90 (381)
43 PF10571 UPF0547: Uncharacteri 94.9 0.0077 1.7E-07 34.3 0.1 23 218-244 1-24 (26)
44 PF04564 U-box: U-box domain; 94.5 0.021 4.5E-07 41.0 1.7 49 107-166 4-52 (73)
45 COG5243 HRD1 HRD ubiquitin lig 94.5 0.035 7.6E-07 51.4 3.3 50 106-164 286-345 (491)
46 KOG0828 Predicted E3 ubiquitin 94.3 0.024 5.1E-07 54.2 2.0 51 107-165 571-635 (636)
47 PF14570 zf-RING_4: RING/Ubox 94.1 0.031 6.7E-07 36.6 1.6 45 110-162 1-46 (48)
48 KOG0802 E3 ubiquitin ligase [P 93.7 0.033 7.2E-07 55.3 1.8 46 107-161 291-338 (543)
49 COG5432 RAD18 RING-finger-cont 93.5 0.036 7.8E-07 49.7 1.5 43 107-161 25-67 (391)
50 KOG2660 Locus-specific chromos 93.3 0.021 4.5E-07 52.1 -0.4 48 106-164 14-61 (331)
51 KOG1814 Predicted E3 ubiquitin 93.0 0.047 1E-06 51.2 1.5 43 216-258 272-317 (445)
52 KOG1645 RING-finger-containing 93.0 0.11 2.3E-06 48.9 3.7 55 107-168 4-60 (463)
53 KOG0824 Predicted E3 ubiquitin 92.5 0.082 1.8E-06 47.7 2.2 52 105-167 5-56 (324)
54 KOG0804 Cytoplasmic Zn-finger 92.3 0.094 2E-06 49.8 2.4 70 104-184 172-248 (493)
55 PF13240 zinc_ribbon_2: zinc-r 91.9 0.048 1E-06 30.0 0.1 12 219-230 1-12 (23)
56 KOG1815 Predicted E3 ubiquitin 91.6 0.12 2.6E-06 50.1 2.4 41 221-261 164-205 (444)
57 PF13248 zf-ribbon_3: zinc-rib 91.5 0.056 1.2E-06 30.6 0.1 23 218-251 3-25 (26)
58 COG5220 TFB3 Cdk activating ki 91.2 0.033 7.2E-07 48.6 -1.6 52 107-164 10-64 (314)
59 smart00661 RPOL9 RNA polymeras 91.2 0.14 3.1E-06 33.8 1.8 27 218-244 1-30 (52)
60 PF05883 Baculo_RING: Baculovi 90.7 0.11 2.3E-06 41.7 0.9 34 107-141 26-66 (134)
61 smart00744 RINGv The RING-vari 89.9 0.43 9.4E-06 31.4 3.2 41 109-155 1-46 (49)
62 KOG4445 Uncharacterized conser 89.7 0.21 4.5E-06 45.1 2.0 41 105-145 113-153 (368)
63 KOG0825 PHD Zn-finger protein 89.5 0.087 1.9E-06 53.2 -0.6 18 128-145 121-138 (1134)
64 KOG3039 Uncharacterized conser 89.4 0.26 5.7E-06 43.3 2.4 56 106-170 220-276 (303)
65 PRK00398 rpoP DNA-directed RNA 89.4 0.42 9.1E-06 30.9 2.8 29 218-246 4-33 (46)
66 PHA00626 hypothetical protein 89.3 0.31 6.7E-06 32.8 2.1 28 219-246 2-35 (59)
67 KOG1952 Transcription factor N 88.9 0.34 7.4E-06 49.5 3.1 54 105-160 189-243 (950)
68 PF13719 zinc_ribbon_5: zinc-r 88.7 0.63 1.4E-05 28.7 3.1 27 218-244 3-35 (37)
69 COG0777 AccD Acetyl-CoA carbox 88.7 0.19 4.1E-06 45.0 1.0 37 214-250 25-63 (294)
70 KOG4185 Predicted E3 ubiquitin 88.6 0.38 8.1E-06 43.8 3.0 48 107-162 3-53 (296)
71 KOG4692 Predicted E3 ubiquitin 88.3 0.3 6.4E-06 45.1 2.0 38 102-142 417-454 (489)
72 TIGR02098 MJ0042_CXXC MJ0042 f 88.1 0.6 1.3E-05 28.7 2.8 26 218-244 3-35 (38)
73 COG5152 Uncharacterized conser 88.1 0.26 5.5E-06 41.9 1.3 34 106-142 195-228 (259)
74 PRK05654 acetyl-CoA carboxylas 88.0 0.13 2.8E-06 47.0 -0.5 31 214-244 24-56 (292)
75 PRK00432 30S ribosomal protein 86.9 0.41 8.9E-06 31.7 1.6 27 217-245 20-48 (50)
76 CHL00174 accD acetyl-CoA carbo 86.3 0.17 3.6E-06 46.2 -0.7 33 214-246 35-69 (296)
77 PF15227 zf-C3HC4_4: zinc fing 86.2 0.24 5.3E-06 31.4 0.2 30 220-254 1-30 (42)
78 PF13717 zinc_ribbon_4: zinc-r 85.9 0.87 1.9E-05 27.9 2.6 27 218-244 3-35 (36)
79 PHA03096 p28-like protein; Pro 85.8 0.4 8.7E-06 43.6 1.4 53 108-163 179-236 (284)
80 TIGR00515 accD acetyl-CoA carb 85.7 0.2 4.3E-06 45.6 -0.6 32 214-245 23-56 (285)
81 KOG0826 Predicted E3 ubiquitin 85.6 1.1 2.4E-05 41.1 4.1 46 107-161 300-345 (357)
82 KOG0297 TNF receptor-associate 85.5 0.59 1.3E-05 44.5 2.5 37 105-143 19-55 (391)
83 PF12861 zf-Apc11: Anaphase-pr 85.3 0.92 2E-05 33.5 2.8 32 126-163 50-81 (85)
84 KOG4739 Uncharacterized protei 85.2 0.38 8.3E-06 42.2 1.0 46 107-164 3-48 (233)
85 PRK14559 putative protein seri 85.0 0.44 9.5E-06 48.2 1.4 34 216-255 14-54 (645)
86 PF08274 PhnA_Zn_Ribbon: PhnA 84.6 0.77 1.7E-05 27.0 1.8 25 219-244 4-29 (30)
87 KOG3579 Predicted E3 ubiquitin 84.4 0.76 1.7E-05 41.3 2.5 69 105-175 266-343 (352)
88 PF09297 zf-NADH-PPase: NADH p 84.0 1.3 2.9E-05 26.2 2.7 27 217-243 3-30 (32)
89 KOG2817 Predicted E3 ubiquitin 83.7 1.2 2.5E-05 42.0 3.5 59 106-170 333-391 (394)
90 PF14952 zf-tcix: Putative tre 82.6 0.55 1.2E-05 29.9 0.6 26 215-244 9-37 (44)
91 COG5175 MOT2 Transcriptional r 82.3 0.65 1.4E-05 42.7 1.2 51 108-167 15-67 (480)
92 KOG4172 Predicted E3 ubiquitin 82.2 0.32 7E-06 32.6 -0.5 46 107-163 7-53 (62)
93 KOG1001 Helicase-like transcri 82.2 0.45 9.7E-06 48.4 0.2 55 108-173 455-509 (674)
94 KOG4265 Predicted E3 ubiquitin 81.5 2 4.4E-05 39.8 4.2 48 105-164 288-336 (349)
95 KOG0317 Predicted E3 ubiquitin 81.2 0.25 5.3E-06 44.4 -1.8 34 217-256 239-273 (293)
96 COG1998 RPS31 Ribosomal protei 80.9 0.95 2.1E-05 29.7 1.3 28 216-243 18-46 (51)
97 PF04641 Rtf2: Rtf2 RING-finge 80.1 1.3 2.9E-05 39.7 2.5 60 105-174 111-171 (260)
98 KOG1734 Predicted RING-contain 80.1 0.55 1.2E-05 41.9 0.0 53 106-165 223-282 (328)
99 KOG4159 Predicted E3 ubiquitin 78.3 1.4 3.1E-05 41.9 2.2 46 107-164 84-129 (398)
100 PLN03208 E3 ubiquitin-protein 77.2 0.56 1.2E-05 40.0 -0.8 34 215-253 16-49 (193)
101 PF09538 FYDLN_acid: Protein o 76.7 1.2 2.5E-05 34.6 0.9 26 218-244 10-36 (108)
102 KOG3800 Predicted E3 ubiquitin 76.4 2 4.4E-05 38.7 2.5 48 109-164 2-51 (300)
103 KOG0827 Predicted E3 ubiquitin 75.1 1.4 3.1E-05 41.2 1.2 37 107-143 4-41 (465)
104 PF10367 Vps39_2: Vacuolar sor 74.8 1.6 3.4E-05 33.1 1.2 32 106-138 77-108 (109)
105 PF14803 Nudix_N_2: Nudix N-te 74.1 3.4 7.3E-05 25.0 2.3 26 218-243 1-31 (34)
106 COG5222 Uncharacterized conser 74.1 2.4 5.3E-05 38.4 2.3 45 107-161 274-318 (427)
107 KOG1785 Tyrosine kinase negati 73.8 1.2 2.5E-05 42.0 0.3 46 107-160 369-414 (563)
108 KOG2906 RNA polymerase III sub 73.7 3 6.5E-05 31.5 2.4 29 219-247 3-34 (105)
109 COG1198 PriA Primosomal protei 73.5 2.6 5.7E-05 43.3 2.7 34 218-251 445-484 (730)
110 KOG0823 Predicted E3 ubiquitin 72.8 0.99 2.1E-05 39.4 -0.4 17 240-256 65-81 (230)
111 PF07800 DUF1644: Protein of u 72.4 9.3 0.0002 31.6 5.1 71 107-179 2-110 (162)
112 PLN03086 PRLI-interacting fact 72.3 1.7 3.8E-05 43.2 1.1 31 150-185 432-462 (567)
113 PF07282 OrfB_Zn_ribbon: Putat 71.5 2.6 5.7E-05 29.4 1.6 29 216-244 27-56 (69)
114 KOG3002 Zn finger protein [Gen 71.3 4.3 9.3E-05 37.2 3.3 46 105-164 46-91 (299)
115 PF05605 zf-Di19: Drought indu 71.1 4.1 9E-05 27.1 2.4 46 107-169 2-47 (54)
116 PRK08665 ribonucleotide-diphos 71.1 2.1 4.6E-05 44.3 1.5 26 218-245 725-751 (752)
117 PF02150 RNA_POL_M_15KD: RNA p 70.4 4.7 0.0001 24.5 2.3 27 218-244 2-30 (35)
118 PF01599 Ribosomal_S27: Riboso 70.1 3.5 7.6E-05 26.9 1.8 27 216-242 17-46 (47)
119 PF06677 Auto_anti-p27: Sjogre 67.9 4.9 0.00011 25.4 2.1 22 218-241 18-41 (41)
120 COG1645 Uncharacterized Zn-fin 66.7 4.2 9.1E-05 32.5 2.0 24 217-249 28-51 (131)
121 PF03119 DNA_ligase_ZBD: NAD-d 66.6 6.6 0.00014 22.5 2.3 20 219-238 1-20 (28)
122 TIGR01384 TFS_arch transcripti 66.5 3.1 6.8E-05 31.6 1.2 24 219-244 2-26 (104)
123 PF07191 zinc-ribbons_6: zinc- 65.7 5.8 0.00013 28.1 2.3 35 219-255 3-43 (70)
124 PRK14892 putative transcriptio 65.3 5.9 0.00013 30.1 2.5 47 215-261 19-69 (99)
125 KOG1813 Predicted E3 ubiquitin 65.0 2.8 6.2E-05 37.9 0.8 34 106-142 240-273 (313)
126 COG1997 RPL43A Ribosomal prote 64.5 5.5 0.00012 29.4 2.1 29 216-244 34-63 (89)
127 KOG0825 PHD Zn-finger protein 63.8 11 0.00023 38.8 4.6 49 108-165 124-172 (1134)
128 PF14445 Prok-RING_2: Prokaryo 63.0 1.4 3E-05 29.0 -1.1 34 107-140 7-40 (57)
129 KOG0006 E3 ubiquitin-protein l 62.0 3.7 7.9E-05 37.6 1.0 42 215-256 313-358 (446)
130 COG5219 Uncharacterized conser 62.0 2.5 5.3E-05 44.2 -0.1 52 106-164 1468-1523(1525)
131 PF14446 Prok-RING_1: Prokaryo 62.0 9.6 0.00021 25.6 2.7 33 107-139 5-38 (54)
132 PF12773 DZR: Double zinc ribb 61.8 2.8 6.1E-05 27.2 0.2 12 217-228 12-23 (50)
133 PF14569 zf-UDP: Zinc-binding 60.6 11 0.00024 27.3 3.0 51 105-163 7-61 (80)
134 PF15616 TerY-C: TerY-C metal 60.3 6.3 0.00014 31.6 1.9 26 216-247 76-101 (131)
135 PLN03086 PRLI-interacting fact 59.8 9.1 0.0002 38.2 3.3 29 216-244 432-463 (567)
136 PF14447 Prok-RING_4: Prokaryo 59.5 4.2 9.2E-05 27.4 0.7 46 107-166 7-52 (55)
137 PF01363 FYVE: FYVE zinc finge 59.4 3.7 8.1E-05 28.6 0.5 36 106-141 8-44 (69)
138 PRK09710 lar restriction allev 58.8 8.1 0.00018 26.9 2.0 28 216-243 5-36 (64)
139 KOG1701 Focal adhesion adaptor 58.6 3.8 8.3E-05 39.0 0.5 37 217-253 394-438 (468)
140 PF08271 TF_Zn_Ribbon: TFIIB z 58.5 11 0.00023 23.8 2.5 24 219-242 2-27 (43)
141 TIGR00686 phnA alkylphosphonat 58.1 7 0.00015 30.1 1.7 27 218-245 3-30 (109)
142 PF08746 zf-RING-like: RING-li 57.2 4.8 0.0001 25.6 0.6 41 110-155 1-41 (43)
143 PF06844 DUF1244: Protein of u 56.8 8.4 0.00018 26.9 1.8 17 131-147 11-27 (68)
144 TIGR02443 conserved hypothetic 56.7 12 0.00025 25.7 2.4 27 218-244 10-41 (59)
145 TIGR02300 FYDLN_acid conserved 56.6 5.6 0.00012 31.6 1.1 26 218-244 10-36 (129)
146 PF10122 Mu-like_Com: Mu-like 56.5 4 8.8E-05 27.0 0.2 25 218-242 5-32 (51)
147 PRK00420 hypothetical protein; 56.4 7.4 0.00016 30.3 1.7 28 217-253 23-51 (112)
148 PRK10220 hypothetical protein; 56.1 8.9 0.00019 29.6 2.0 27 218-245 4-31 (111)
149 PF08792 A2L_zn_ribbon: A2L zi 55.4 16 0.00035 21.8 2.7 28 217-244 3-31 (33)
150 KOG1941 Acetylcholine receptor 55.0 3.9 8.4E-05 38.5 -0.1 48 107-161 365-413 (518)
151 PF04216 FdhE: Protein involve 54.6 1.9 4.1E-05 39.2 -2.2 39 150-190 171-211 (290)
152 TIGR01206 lysW lysine biosynth 54.4 14 0.0003 24.9 2.5 28 218-245 3-33 (54)
153 COG1594 RPB9 DNA-directed RNA 54.2 10 0.00023 29.5 2.2 27 218-244 3-32 (113)
154 PRK04023 DNA polymerase II lar 53.9 10 0.00023 40.1 2.7 33 216-254 625-663 (1121)
155 PF06906 DUF1272: Protein of u 53.7 16 0.00034 24.7 2.7 46 107-165 5-53 (57)
156 PF09526 DUF2387: Probable met 53.5 13 0.00028 26.5 2.4 27 218-244 9-40 (71)
157 PF12906 RINGv: RING-variant d 53.2 16 0.00035 23.6 2.7 33 110-143 1-38 (47)
158 KOG1812 Predicted E3 ubiquitin 52.8 4.3 9.3E-05 38.6 -0.2 63 217-279 235-303 (384)
159 PF13453 zf-TFIIB: Transcripti 52.1 10 0.00022 23.7 1.5 13 219-231 1-13 (41)
160 TIGR00595 priA primosomal prot 51.9 11 0.00023 37.3 2.4 34 218-251 223-262 (505)
161 KOG0801 Predicted E3 ubiquitin 51.5 6.2 0.00013 32.7 0.6 28 106-133 176-203 (205)
162 smart00659 RPOLCX RNA polymera 51.3 15 0.00033 23.5 2.3 24 219-243 4-28 (44)
163 PF07975 C1_4: TFIIH C1-like d 51.2 8.2 0.00018 25.6 1.0 16 122-137 21-36 (51)
164 PF05290 Baculo_IE-1: Baculovi 51.0 14 0.0003 29.6 2.4 53 106-164 79-132 (140)
165 KOG1940 Zn-finger protein [Gen 50.8 10 0.00022 34.4 1.8 46 107-161 158-204 (276)
166 PF12861 zf-Apc11: Anaphase-pr 50.8 4.7 0.0001 29.7 -0.2 35 218-255 33-67 (85)
167 TIGR03655 anti_R_Lar restricti 50.4 11 0.00024 25.0 1.6 11 218-228 2-12 (53)
168 PRK11827 hypothetical protein; 50.3 13 0.00028 25.6 1.9 27 217-243 8-35 (60)
169 PF15446 zf-PHD-like: PHD/FYVE 49.8 5 0.00011 33.4 -0.2 12 177-188 125-136 (175)
170 COG5574 PEX10 RING-finger-cont 49.3 3.1 6.7E-05 37.1 -1.6 32 217-254 215-248 (271)
171 COG5432 RAD18 RING-finger-cont 49.1 5.1 0.00011 36.3 -0.3 35 218-259 26-62 (391)
172 KOG0309 Conserved WD40 repeat- 48.1 14 0.0003 37.9 2.5 47 105-160 1026-1072(1081)
173 PRK14714 DNA polymerase II lar 47.7 12 0.00025 40.7 2.0 30 218-253 668-703 (1337)
174 PRK12286 rpmF 50S ribosomal pr 47.6 13 0.00027 25.3 1.5 22 215-241 25-47 (57)
175 PHA02929 N1R/p28-like protein; 46.9 7.5 0.00016 34.5 0.4 39 216-254 173-214 (238)
176 PRK14873 primosome assembly pr 46.9 15 0.00032 37.6 2.6 34 218-251 393-431 (665)
177 PF08882 Acetone_carb_G: Aceto 45.2 18 0.00039 28.0 2.2 13 234-246 23-35 (112)
178 PF10272 Tmpp129: Putative tra 45.2 26 0.00056 33.0 3.7 35 128-164 311-351 (358)
179 PF05129 Elf1: Transcription e 44.9 17 0.00038 26.5 2.0 32 216-247 21-59 (81)
180 smart00064 FYVE Protein presen 44.8 9.8 0.00021 26.3 0.7 37 107-143 10-47 (68)
181 PF02891 zf-MIZ: MIZ/SP-RING z 44.3 35 0.00075 22.3 3.2 47 108-161 3-49 (50)
182 TIGR01031 rpmF_bact ribosomal 43.6 15 0.00033 24.7 1.5 22 215-241 24-46 (55)
183 COG1096 Predicted RNA-binding 43.1 19 0.00041 30.6 2.2 24 218-243 150-174 (188)
184 KOG4275 Predicted E3 ubiquitin 42.3 11 0.00025 34.1 0.8 30 107-139 300-330 (350)
185 PF14149 YhfH: YhfH-like prote 42.2 1.8 4E-05 26.6 -2.9 28 213-240 9-37 (37)
186 PHA02926 zinc finger-like prot 42.2 9.6 0.00021 33.3 0.4 43 213-255 166-212 (242)
187 COG3492 Uncharacterized protei 42.1 19 0.00041 26.8 1.8 17 131-147 42-58 (104)
188 KOG3161 Predicted E3 ubiquitin 42.1 6.1 0.00013 39.6 -1.0 38 106-143 10-48 (861)
189 PRK05580 primosome assembly pr 41.8 18 0.0004 37.0 2.4 33 219-251 392-430 (679)
190 PF06827 zf-FPG_IleRS: Zinc fi 41.6 15 0.00032 21.1 1.0 24 218-241 2-28 (30)
191 smart00834 CxxC_CXXC_SSSS Puta 41.6 18 0.00038 22.1 1.4 11 219-229 7-17 (41)
192 COG3813 Uncharacterized protei 41.5 23 0.00051 25.2 2.1 47 107-165 5-53 (84)
193 PF12760 Zn_Tnp_IS1595: Transp 41.1 56 0.0012 20.8 3.8 25 218-242 19-45 (46)
194 KOG2034 Vacuolar sorting prote 41.0 16 0.00035 38.0 1.8 40 105-145 815-854 (911)
195 TIGR01053 LSD1 zinc finger dom 41.0 30 0.00066 20.4 2.3 24 219-242 3-27 (31)
196 KOG2930 SCF ubiquitin ligase, 40.2 18 0.0004 27.6 1.5 26 126-158 79-104 (114)
197 PF14471 DUF4428: Domain of un 39.1 27 0.00058 23.1 2.0 30 109-140 1-30 (51)
198 PF04216 FdhE: Protein involve 38.9 18 0.0004 32.8 1.7 35 218-252 173-221 (290)
199 PRK14559 putative protein seri 38.8 14 0.00031 37.6 1.0 33 218-254 2-39 (645)
200 PF01783 Ribosomal_L32p: Ribos 38.6 15 0.00033 24.7 0.8 14 215-228 24-37 (56)
201 COG5109 Uncharacterized conser 38.4 30 0.00065 31.9 2.9 55 106-166 335-389 (396)
202 PRK13130 H/ACA RNA-protein com 38.1 43 0.00093 22.7 2.9 38 216-275 4-41 (56)
203 PF09788 Tmemb_55A: Transmembr 38.0 18 0.00039 32.2 1.4 38 149-186 121-167 (256)
204 PF03604 DNA_RNApol_7kD: DNA d 37.4 13 0.00027 22.2 0.2 22 220-242 3-25 (32)
205 PF14353 CpXC: CpXC protein 37.3 39 0.00084 26.5 3.1 39 152-192 2-54 (128)
206 PF14354 Lar_restr_allev: Rest 37.0 34 0.00073 23.0 2.4 12 216-227 2-13 (61)
207 PF06943 zf-LSD1: LSD1 zinc fi 36.8 40 0.00087 18.9 2.2 23 220-242 1-24 (25)
208 KOG3039 Uncharacterized conser 36.8 30 0.00064 30.8 2.5 35 107-144 43-77 (303)
209 COG5236 Uncharacterized conser 36.1 23 0.00049 33.0 1.8 34 104-140 58-91 (493)
210 PRK09521 exosome complex RNA-b 35.8 29 0.00064 29.3 2.4 26 218-244 150-176 (189)
211 KOG3268 Predicted E3 ubiquitin 35.2 44 0.00094 28.2 3.1 58 105-164 163-228 (234)
212 PF01873 eIF-5_eIF-2B: Domain 35.1 42 0.00091 26.6 3.0 35 207-243 85-123 (125)
213 TIGR01562 FdhE formate dehydro 35.0 37 0.00081 31.2 3.0 38 150-189 183-223 (305)
214 KOG3053 Uncharacterized conser 34.9 25 0.00053 31.4 1.7 55 106-162 19-80 (293)
215 PF12677 DUF3797: Domain of un 34.1 37 0.0008 22.2 2.0 29 216-244 12-48 (49)
216 KOG4367 Predicted Zn-finger pr 34.1 20 0.00043 34.4 1.1 35 106-143 3-37 (699)
217 KOG4684 Uncharacterized conser 34.1 25 0.00055 30.5 1.6 38 149-186 136-180 (275)
218 PRK14714 DNA polymerase II lar 33.6 28 0.00062 37.9 2.3 11 244-254 711-721 (1337)
219 cd00065 FYVE FYVE domain; Zinc 33.6 30 0.00065 22.7 1.7 35 108-142 3-38 (57)
220 PF00628 PHD: PHD-finger; Int 33.4 27 0.00059 22.4 1.4 46 109-155 1-46 (51)
221 PF02318 FYVE_2: FYVE-type zin 33.1 32 0.00068 26.8 2.0 33 107-139 54-88 (118)
222 COG2816 NPY1 NTP pyrophosphohy 33.0 35 0.00075 31.0 2.4 29 216-244 110-139 (279)
223 PF02148 zf-UBP: Zn-finger in 32.8 52 0.0011 22.4 2.8 32 110-143 1-36 (63)
224 KOG2807 RNA polymerase II tran 32.7 23 0.00049 32.8 1.2 29 110-138 333-361 (378)
225 smart00653 eIF2B_5 domain pres 32.4 73 0.0016 24.7 3.8 34 207-242 72-109 (110)
226 PF03833 PolC_DP2: DNA polymer 32.1 15 0.00033 38.2 0.0 33 216-254 654-692 (900)
227 PF07754 DUF1610: Domain of un 32.1 33 0.00072 19.0 1.4 8 217-224 16-23 (24)
228 KOG0298 DEAD box-containing he 31.8 18 0.00039 39.3 0.5 37 106-144 1152-1188(1394)
229 PF08646 Rep_fac-A_C: Replicat 31.2 50 0.0011 26.5 3.0 26 217-243 18-46 (146)
230 KOG2979 Protein involved in DN 31.1 24 0.00052 31.5 1.1 47 107-160 176-222 (262)
231 PRK03988 translation initiatio 30.5 77 0.0017 25.6 3.8 35 207-243 94-132 (138)
232 PRK00241 nudC NADH pyrophospha 30.2 49 0.0011 29.6 2.9 29 216-244 98-127 (256)
233 KOG2932 E3 ubiquitin ligase in 30.1 38 0.00083 31.1 2.2 32 107-140 90-121 (389)
234 PF07227 DUF1423: Protein of u 29.9 26 0.00057 33.8 1.2 34 151-184 97-131 (446)
235 COG1996 RPC10 DNA-directed RNA 29.9 34 0.00074 22.5 1.4 19 220-238 9-27 (49)
236 cd04476 RPA1_DBD_C RPA1_DBD_C: 29.9 36 0.00078 28.0 1.9 26 217-243 34-60 (166)
237 TIGR00311 aIF-2beta translatio 29.9 84 0.0018 25.2 3.9 35 207-243 89-127 (133)
238 KOG1571 Predicted E3 ubiquitin 29.7 13 0.00028 34.7 -0.9 43 106-163 304-346 (355)
239 PRK12496 hypothetical protein; 29.4 29 0.00062 28.9 1.2 31 215-254 124-155 (164)
240 PF02591 DUF164: Putative zinc 29.3 53 0.0011 21.8 2.3 30 153-184 24-54 (56)
241 PF11781 RRN7: RNA polymerase 28.2 55 0.0012 19.9 2.0 24 218-243 9-34 (36)
242 PHA02825 LAP/PHD finger-like p 27.7 60 0.0013 26.9 2.7 52 106-166 7-61 (162)
243 PRK12336 translation initiatio 27.1 91 0.002 26.8 4.0 39 207-247 90-132 (201)
244 PF01780 Ribosomal_L37ae: Ribo 26.9 47 0.001 24.8 1.8 29 216-244 34-63 (90)
245 PF11809 DUF3330: Domain of un 26.4 33 0.00072 24.1 0.9 38 107-144 11-51 (70)
246 PRK08332 ribonucleotide-diphos 26.4 38 0.00083 38.4 1.9 27 218-246 1705-1738(1740)
247 PF02318 FYVE_2: FYVE-type zin 26.4 64 0.0014 25.1 2.7 35 216-251 53-88 (118)
248 smart00249 PHD PHD zinc finger 26.2 47 0.001 20.1 1.6 32 109-140 1-32 (47)
249 PF03884 DUF329: Domain of unk 26.1 47 0.001 22.6 1.6 16 217-232 2-17 (57)
250 COG2824 PhnA Uncharacterized Z 25.8 51 0.0011 25.3 1.9 26 218-244 4-30 (112)
251 PF00098 zf-CCHC: Zinc knuckle 25.6 44 0.00095 17.0 1.1 16 178-193 2-17 (18)
252 PLN02436 cellulose synthase A 25.5 1E+02 0.0022 33.3 4.6 51 106-164 35-89 (1094)
253 COG4640 Predicted membrane pro 25.0 31 0.00067 32.8 0.7 8 218-225 2-9 (465)
254 COG5194 APC11 Component of SCF 24.6 88 0.0019 22.8 2.8 24 126-156 52-75 (88)
255 COG0266 Nei Formamidopyrimidin 24.3 55 0.0012 29.7 2.1 24 217-240 245-271 (273)
256 PF07649 C1_3: C1-like domain; 23.8 55 0.0012 18.7 1.4 29 108-136 1-29 (30)
257 PF06467 zf-FCS: MYM-type Zinc 23.7 67 0.0015 19.7 1.9 35 106-140 5-43 (43)
258 PF05715 zf-piccolo: Piccolo Z 23.1 29 0.00063 23.7 0.1 35 218-252 3-40 (61)
259 TIGR00570 cdk7 CDK-activating 23.0 30 0.00064 31.9 0.2 34 218-251 4-37 (309)
260 PRK12495 hypothetical protein; 22.9 71 0.0015 27.9 2.5 30 216-254 41-70 (226)
261 PRK08115 ribonucleotide-diphos 22.9 40 0.00086 35.5 1.1 24 218-243 828-853 (858)
262 TIGR00599 rad18 DNA repair pro 22.8 19 0.00041 34.4 -1.2 33 217-254 26-58 (397)
263 PF09862 DUF2089: Protein of u 22.5 70 0.0015 25.0 2.1 9 220-228 1-9 (113)
264 PF10497 zf-4CXXC_R1: Zinc-fin 22.4 1.5E+02 0.0033 22.6 4.0 31 129-161 37-69 (105)
265 PLN02189 cellulose synthase 22.3 1.2E+02 0.0027 32.6 4.5 51 106-164 33-87 (1040)
266 KOG2114 Vacuolar assembly/sort 22.2 52 0.0011 34.4 1.7 41 107-161 840-880 (933)
267 PRK03564 formate dehydrogenase 22.1 74 0.0016 29.4 2.6 38 150-189 186-225 (309)
268 PRK00564 hypA hydrogenase nick 22.1 72 0.0016 24.9 2.2 10 217-226 88-97 (117)
269 KOG1493 Anaphase-promoting com 22.0 19 0.00042 26.0 -1.0 49 107-161 20-78 (84)
270 KOG2879 Predicted E3 ubiquitin 21.9 38 0.00082 30.6 0.6 30 217-251 239-269 (298)
271 PF13834 DUF4193: Domain of un 21.4 51 0.0011 25.0 1.1 30 106-136 69-98 (99)
272 KOG2164 Predicted E3 ubiquitin 21.1 26 0.00057 34.3 -0.6 31 217-252 186-216 (513)
273 PF00412 LIM: LIM domain; Int 21.0 84 0.0018 20.4 2.1 32 107-140 26-57 (58)
274 PRK11088 rrmA 23S rRNA methylt 20.6 58 0.0013 29.0 1.6 24 219-244 4-27 (272)
275 PRK03564 formate dehydrogenase 20.6 59 0.0013 30.0 1.6 33 218-250 188-234 (309)
276 PF10764 Gin: Inhibitor of sig 20.4 53 0.0012 21.2 0.9 35 109-147 1-35 (46)
277 PF09151 DUF1936: Domain of un 20.0 38 0.00082 19.9 0.1 9 219-227 3-11 (36)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=3.2e-30 Score=241.44 Aligned_cols=151 Identities=36% Similarity=0.858 Sum_probs=130.1
Q ss_pred CCCccccccc-ccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhhCCCCc-------
Q 048441 105 DPSFVCEICV-ESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNILPQQV------- 176 (292)
Q Consensus 105 ~~~~~C~IC~-~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~------- 176 (292)
....+|.||+ +.....+++.+..|+|.||.+|+++||+.+ ......+.||..+|...++.+.+..+|++++
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 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQR 222 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHH
Confidence 4579999999 444444677778999999999999999999 4445889999999999999998888887521
Q ss_pred --------------------------------------------eeccCCCCCccCCCCchhHHHhcccchhHHHHHHHH
Q 048441 177 --------------------------------------------MFCAKCKVPWHTDMKCEDFQNLNENENDDIKLKKLA 212 (292)
Q Consensus 177 --------------------------------------------~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~ 212 (292)
.||..|+.+||.+++|++|+++......+..+.+++
T Consensus 223 ~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~l 302 (384)
T KOG1812|consen 223 LKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYL 302 (384)
T ss_pred HHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHH
Confidence 899999999999999999999998765555666666
Q ss_pred HhCCeeecCCCCeeEEecCCcCeEEeccCcceeeccccCccCCCC
Q 048441 213 VEMKWKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSELYP 257 (292)
Q Consensus 213 ~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~~~ 257 (292)
. +.|+.||+|+..|++++|||||+|+||++|||.|+.+|..+..
T Consensus 303 a-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 303 A-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred H-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCc
Confidence 6 7899999999999999999999999999999999999976553
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=2.4e-29 Score=228.48 Aligned_cols=158 Identities=30% Similarity=0.686 Sum_probs=129.8
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcC-ccccCCCCCCCCCCCCHHHHHhhCCCCc--------
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQES-ITTIGCPVTGCQGVLEPEYCRNILPQQV-------- 176 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~~l~~~~-------- 176 (292)
..+.|.|||++..+...+..++|+|+||+.|++.|+...|+++ +..++||.++|+...++..++.++..++
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~ 262 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKLM 262 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHHH
Confidence 3799999999999888888899999999999999999999988 4679999999999999888888776543
Q ss_pred ---------------------------------------eeccCCCCCccCCCCchhH--------HHhcccch------
Q 048441 177 ---------------------------------------MFCAKCKVPWHTDMKCEDF--------QNLNENEN------ 203 (292)
Q Consensus 177 ---------------------------------------~~C~~C~~~~H~~~~C~~~--------~~~~~~~~------ 203 (292)
.||..|+..||+...|.-- ..+...+.
T Consensus 263 lqk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~el 342 (445)
T KOG1814|consen 263 LQKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEARKREL 342 (445)
T ss_pred HHHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHH
Confidence 8999999999999899521 11211100
Q ss_pred -------------hHHHHHHHHHhCCeeecCCCCeeEEecCCcCeEEe-ccCcceeeccccCccCCCCCCCCCcc
Q 048441 204 -------------DDIKLKKLAVEMKWKRCPNCGYYVEKFRGCNIIIC-RCGTSFHYYSRADLSELYPYRPASRQ 264 (292)
Q Consensus 204 -------------~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~~~y~~~~~~ 264 (292)
++.+..+|+. .+.|+||+|+++|||++|||+|+| .|++.|||+|+..+.+.+||+||++.
T Consensus 343 e~Ryg~rvve~~vn~~lsekwl~-~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 343 EKRYGKRVVEELVNDFLSEKWLE-SNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHH-hcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 1111112222 467999999999999999999999 89999999999999999999999964
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.2e-24 Score=208.64 Aligned_cols=180 Identities=26% Similarity=0.516 Sum_probs=144.0
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccc-cCCCCCCCCCCCCHHHHHhhCCCC-c--------
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITT-IGCPVTGCQGVLEPEYCRNILPQQ-V-------- 176 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~-i~CP~~~C~~~l~~~~i~~~l~~~-~-------- 176 (292)
...|.||++.... . +..+.|||.||..||..||..+|..+... |+||..+|...+..+.|..+++.. .
T Consensus 70 ~~~c~ic~~~~~~-~-~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i 147 (444)
T KOG1815|consen 70 DVQCGICVESYDG-E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYI 147 (444)
T ss_pred cccCCcccCCCcc-h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHH
Confidence 6999999998765 3 33459999999999999999999876433 999999999998877777666652 1
Q ss_pred ---------------------------------------eeccCCCCCccCCCCchhHHHhcccchhHHHHHHHHHhCCe
Q 048441 177 ---------------------------------------MFCAKCKVPWHTDMKCEDFQNLNENENDDIKLKKLAVEMKW 217 (292)
Q Consensus 177 ---------------------------------------~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (292)
.||+.|+.+||.+.+|.....|.+...++.....|+. .++
T Consensus 148 ~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~-~nt 226 (444)
T KOG1815|consen 148 LRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWIL-ANT 226 (444)
T ss_pred HHHHHhcCCccccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhh-ccC
Confidence 4899999999999999999999998777766666665 468
Q ss_pred eecCCCCeeEEecCCcCeEEe-c--cCcceeeccccCccCCCC---C--CCCCccc--C-CCCCCCChhhhhhhcccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-R--CGTSFHYYSRADLSELYP---Y--RPASRQK--G-FRLKSRDPVRTLEYFDFLDL 286 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~~~~---y--~~~~~~~--~-~~~~~~~~~~~l~~~~~~~~ 286 (292)
++||+|.++|||++|||||+| . |+++|||+|++.|..|.. | .+|.... + .+....+..+|.+|+++|..
T Consensus 227 k~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~~ 306 (444)
T KOG1815|consen 227 KECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWME 306 (444)
T ss_pred ccCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHHh
Confidence 889999999999999999999 4 999999999999998742 2 2443211 1 22233456679999999876
Q ss_pred CCC
Q 048441 287 PEG 289 (292)
Q Consensus 287 ~~~ 289 (292)
+.+
T Consensus 307 ~q~ 309 (444)
T KOG1815|consen 307 HQV 309 (444)
T ss_pred hhh
Confidence 654
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=3.2e-18 Score=151.22 Aligned_cols=152 Identities=23% Similarity=0.541 Sum_probs=100.8
Q ss_pred CCCcccccccccCCCCCceeecCCC--CccchhhHHHHHHHHHhcC----------------------------------
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCS--HSYCTDCIIKYVASKLQES---------------------------------- 148 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~Cg--H~fC~~Cl~~~i~~~i~~~---------------------------------- 148 (292)
....+|..|-+-- +.+-+.+|. |+.|.+|++.|..+.+++.
T Consensus 219 ~~ni~C~~Ctdv~---~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~agc~~s~i~e~HHF~ilg~ 295 (446)
T KOG0006|consen 219 SRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGE 295 (446)
T ss_pred cccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccCCCchHHHHhhhhheecch
Confidence 3578999998632 233345788 9999999999999887542
Q ss_pred -----------------ccccCCCCCCCCCCCCHH-HHHhhCCCC---ceeccCCCCCccCCCCchhHHHhc--------
Q 048441 149 -----------------ITTIGCPVTGCQGVLEPE-YCRNILPQQ---VMFCAKCKVPWHTDMKCEDFQNLN-------- 199 (292)
Q Consensus 149 -----------------~~~i~CP~~~C~~~l~~~-~i~~~l~~~---~~~C~~C~~~~H~~~~C~~~~~~~-------- 199 (292)
...+.||.++|+..|-++ +.++..-.. ..||..|+..+|.+ .|.+.-...
T Consensus 296 e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~tc~y~ 374 (446)
T KOG0006|consen 296 EQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTTTCAYR 374 (446)
T ss_pred hHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccc-cceeeeccccccceeee
Confidence 024566666666544332 222222111 18999999999987 454211100
Q ss_pred cc------chhHHHHHHHHHhCCeeecCCCCeeEEecCCcCeEEe-c--cCcceeeccccCccCCCCCCCC
Q 048441 200 EN------ENDDIKLKKLAVEMKWKRCPNCGYYVEKFRGCNIIIC-R--CGTSFHYYSRADLSELYPYRPA 261 (292)
Q Consensus 200 ~~------~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~~~~y~~~ 261 (292)
-. .+=+. ..+...+..+|+||+|++++||++||.||.| + ||.+|||.|+.+|....-..||
T Consensus 375 vde~~a~~arwd~-as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHW 444 (446)
T KOG0006|consen 375 VDERAAEQARWDA-ASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHW 444 (446)
T ss_pred cChhhhhhhhhhh-hhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccccc
Confidence 00 01111 1122234578999999999999999999999 5 9999999999999976555554
No 5
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.04 E-value=5.4e-10 Score=92.02 Aligned_cols=57 Identities=26% Similarity=0.695 Sum_probs=46.1
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhh
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNI 171 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 171 (292)
...+.|+||++.+.....++ +.|||+||..|++..++ ...+|| .|++.|+..++..+
T Consensus 129 ~~~~~CPiCl~~~sek~~vs-TkCGHvFC~~Cik~alk-------~~~~CP--~C~kkIt~k~~~rI 185 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVS-TKCGHVFCSQCIKDALK-------NTNKCP--TCRKKITHKQFHRI 185 (187)
T ss_pred ccccCCCceecchhhccccc-cccchhHHHHHHHHHHH-------hCCCCC--Ccccccchhhheec
Confidence 34799999999887655443 48999999999999998 568999 68888887766544
No 6
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.51 E-value=2.1e-07 Score=65.05 Aligned_cols=48 Identities=27% Similarity=0.633 Sum_probs=40.2
Q ss_pred HHHHHHHh-CCeeecC--CCCeeEEecC--CcCeEEe-ccCcceeeccccCccC
Q 048441 207 KLKKLAVE-MKWKRCP--NCGYYVEKFR--GCNIIIC-RCGTSFHYYSRADLSE 254 (292)
Q Consensus 207 ~~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~~FC~~C~~~~~~ 254 (292)
++..++.. ..++.|| +|+..|+..+ |..+|+| .|++.|||.|+.+|+.
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 34444443 5788999 9999999975 9999999 8999999999999965
No 7
>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=98.48 E-value=5.5e-08 Score=63.05 Aligned_cols=41 Identities=29% Similarity=0.688 Sum_probs=32.9
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCC
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPV 156 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 156 (292)
+|+||++++...+.+..+.|+|.||.+||..|++.. ..||.
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 699999999765655566899999999999999852 38883
No 8
>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=98.35 E-value=4.1e-07 Score=57.38 Aligned_cols=38 Identities=37% Similarity=0.989 Sum_probs=29.0
Q ss_pred cccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCC
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPV 156 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 156 (292)
|+||++.+.. .+.++.|||.||.+||.+|++. ..+||.
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~-------~~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEK-------NPKCPV 38 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHC-------TSB-TT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHC-------cCCCcC
Confidence 8999997654 4456799999999999999984 368883
No 9
>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=98.34 E-value=3.8e-07 Score=58.04 Aligned_cols=39 Identities=33% Similarity=0.899 Sum_probs=31.8
Q ss_pred cccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
|+||++.+.... .++.|||.||..||.+|++. ...+.||
T Consensus 1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~-----~~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN-----SGSVKCP 39 (41)
T ss_dssp ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH-----TSSSBTT
T ss_pred CCcCCccccCCC--EEecCCCcchHHHHHHHHHh-----cCCccCC
Confidence 899999765433 46799999999999999997 2567898
No 10
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.28 E-value=6.2e-07 Score=57.68 Aligned_cols=42 Identities=31% Similarity=0.702 Sum_probs=23.4
Q ss_pred cccccccCC-CCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 110 CEICVESKS-PNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 110 C~IC~~~~~-~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
|+||.+ +. ......++.|||.||++|+.++++... ...++||
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 53 344455678999999999999998542 2568887
No 11
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.22 E-value=3.2e-07 Score=64.00 Aligned_cols=39 Identities=41% Similarity=0.943 Sum_probs=29.3
Q ss_pred CeeecCC--CCeeEEecCCcCe--EEe-ccCcceeeccccCccC
Q 048441 216 KWKRCPN--CGYYVEKFRGCNI--IIC-RCGTSFHYYSRADLSE 254 (292)
Q Consensus 216 ~~k~CP~--C~~~iek~~GCnh--m~C-~C~~~FC~~C~~~~~~ 254 (292)
..+.||+ |...+++..|.++ |+| .|++.|||.|+.+|+.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 4579987 9999999999999 999 5999999999999964
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.17 E-value=1.7e-06 Score=56.05 Aligned_cols=43 Identities=33% Similarity=0.838 Sum_probs=35.8
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
.|+||++.+.....+.++.|||.||..|+.... ...+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCc--CCC
Confidence 489999998555667788999999999999988 2678999 465
No 13
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.17 E-value=5.1e-07 Score=57.90 Aligned_cols=40 Identities=25% Similarity=0.727 Sum_probs=26.4
Q ss_pred cccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
|+||++.+. +.++ +.|||.||..||..+++..- ...+.||
T Consensus 1 CpiC~~~~~--~Pv~-l~CGH~FC~~Cl~~~~~~~~---~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFK--DPVS-LPCGHSFCRSCLERLWKEPS---GSGFSCP 40 (42)
T ss_dssp ETTTTSB-S--SEEE--SSSSEEEHHHHHHHHCCSS---SST---S
T ss_pred CCccchhhC--Cccc-cCCcCHHHHHHHHHHHHccC---CcCCCCc
Confidence 899999765 3344 48999999999999987421 1237888
No 14
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.13 E-value=3.2e-06 Score=53.96 Aligned_cols=44 Identities=34% Similarity=0.793 Sum_probs=34.0
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCC
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGV 162 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 162 (292)
+|+||++.+ ...+.+..|||.||..|+..|+.. ....|| .|+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence 599999977 334445579999999999999885 457798 57654
No 15
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.06 E-value=3.4e-06 Score=71.42 Aligned_cols=63 Identities=22% Similarity=0.527 Sum_probs=46.4
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHH---------hcCccccCCCCCCCCCCCCHHHHHhhCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKL---------QESITTIGCPVTGCQGVLEPEYCRNILPQ 174 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i---------~~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 174 (292)
.++|+||++.+.. .+ ++.|||.||..|+..|+...- ........|| .|+..+....+..+...
T Consensus 18 ~~~CpICld~~~d--PV-vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiygr 89 (193)
T PLN03208 18 DFDCNICLDQVRD--PV-VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYGR 89 (193)
T ss_pred ccCCccCCCcCCC--cE-EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeecc
Confidence 6999999997643 22 358999999999999986421 1123467999 79999988777666543
No 16
>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=97.87 E-value=1.5e-05 Score=53.02 Aligned_cols=46 Identities=26% Similarity=0.724 Sum_probs=35.4
Q ss_pred CcccccccccCCCCCceeecCCCCc-cchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHS-YCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
...|.||++... + +.+.+|||. ||..|+..++. ...+|| .|+..+.
T Consensus 2 ~~~C~iC~~~~~--~-~~~~pCgH~~~C~~C~~~~~~-------~~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--D-VVLLPCGHLCFCEECAERLLK-------RKKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--S-EEEETTCEEEEEHHHHHHHHH-------TTSBBT--TTTBB-S
T ss_pred cCCCccCCccCC--c-eEEeCCCChHHHHHHhHHhcc-------cCCCCC--cCChhhc
Confidence 478999999643 2 345699999 99999999998 568999 6887654
No 17
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.84 E-value=1.6e-05 Score=69.92 Aligned_cols=49 Identities=27% Similarity=0.610 Sum_probs=37.4
Q ss_pred CcccccccccCCCCC-----ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNE-----SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~-----~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
..+|+||++.+.... ...++.|+|.||.+|+..|+. ....|| .|+..+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-------~~~tCP--lCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-------EKNTCP--VCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-------cCCCCC--CCCCEee
Confidence 689999999865432 233568999999999999986 345899 6886554
No 18
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=1.1e-05 Score=76.85 Aligned_cols=58 Identities=24% Similarity=0.590 Sum_probs=44.5
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhh
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNI 171 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 171 (292)
...|||||++.....+ +.|||+||-.||.+|+.... ......|| -|...+.+.+++.+
T Consensus 186 ~~~CPICL~~~~~p~~---t~CGHiFC~~CiLqy~~~s~--~~~~~~CP--iC~s~I~~kdl~pv 243 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR---TNCGHIFCGPCILQYWNYSA--IKGPCSCP--ICRSTITLKDLLPV 243 (513)
T ss_pred CCcCCcccCCCCcccc---cccCceeeHHHHHHHHhhhc--ccCCccCC--chhhhccccceeee
Confidence 7899999997665443 36999999999999999862 22567898 69988887655443
No 19
>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=97.75 E-value=2.8e-05 Score=47.76 Aligned_cols=37 Identities=35% Similarity=0.902 Sum_probs=28.2
Q ss_pred cccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
|+||++.. .....+.|+|.||..|+..|+.. ....||
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~------~~~~CP 37 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKS------GNNTCP 37 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHh------CcCCCC
Confidence 78999872 23344589999999999999881 446787
No 20
>PHA02926 zinc finger-like protein; Provisional
Probab=97.55 E-value=6.6e-05 Score=64.57 Aligned_cols=54 Identities=22% Similarity=0.533 Sum_probs=38.7
Q ss_pred CcccccccccCCC-----CC-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSP-----NE-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 107 ~~~C~IC~~~~~~-----~~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
..+|+||++.+.. .. .-.+..|+|.||..|++.|...+-. ....-.|| -|+..+
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~-~~~~rsCP--iCR~~f 229 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE-TGASDNCP--ICRTRF 229 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc-cCcCCcCC--CCccee
Confidence 5899999997632 22 2234699999999999999986532 22456799 688654
No 21
>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=97.55 E-value=0.00012 Score=50.74 Aligned_cols=49 Identities=24% Similarity=0.261 Sum_probs=37.8
Q ss_pred cccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHH
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYC 168 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 168 (292)
+.|+||.+.+... + ++.|||.||+.|+..|+.. ...|| .|+..+..+++
T Consensus 2 ~~Cpi~~~~~~~P--v-~~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVMKDP--V-ILPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcCCCC--E-ECCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhc
Confidence 6799999976542 3 3589999999999999975 35799 57777766543
No 22
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.53 E-value=5e-05 Score=65.64 Aligned_cols=60 Identities=18% Similarity=0.560 Sum_probs=45.6
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhhCCC
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNILPQ 174 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 174 (292)
..|+|.||+|.-.. .++ +.|||.||=.||-+|+.... ..-.|| .|+..++.+.+-.|...
T Consensus 46 ~~FdCNICLd~akd-PVv--TlCGHLFCWpClyqWl~~~~----~~~~cP--VCK~~Vs~~~vvPlYGr 105 (230)
T KOG0823|consen 46 GFFDCNICLDLAKD-PVV--TLCGHLFCWPCLYQWLQTRP----NSKECP--VCKAEVSIDTVVPLYGR 105 (230)
T ss_pred CceeeeeeccccCC-CEE--eecccceehHHHHHHHhhcC----CCeeCC--ccccccccceEEeeecc
Confidence 37999999996443 233 35999999999999998754 334678 79999988777666553
No 23
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=0.00012 Score=65.09 Aligned_cols=52 Identities=27% Similarity=0.772 Sum_probs=41.0
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYC 168 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 168 (292)
.....|.+|++.... .+.++|||.||-.||..|..++ -.|| -|+..+.+..+
T Consensus 237 ~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek-------~eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEK-------AECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccc-------cCCC--cccccCCCcce
Confidence 457999999997643 2346899999999999999853 4499 69988887654
No 24
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=0.00016 Score=64.69 Aligned_cols=52 Identities=25% Similarity=0.696 Sum_probs=45.5
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
...+|.||++++...+...+++|.|.|.+.|+.+|+.- ...+|| .|+..++|
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~------y~~~CP--vCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG------YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh------hcccCC--ccCCCCCC
Confidence 46999999999987776777899999999999999974 678999 79988875
No 25
>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=97.34 E-value=0.00018 Score=65.38 Aligned_cols=53 Identities=25% Similarity=0.558 Sum_probs=38.2
Q ss_pred CcccccccccCCCCCc--eeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHH
Q 048441 107 SFVCEICVESKSPNES--FRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEY 167 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~--~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 167 (292)
...||+|..+...... +.+..|||.||..|+...+.. ....|| .|+..+....
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~------~~~~CP--~C~~~lrk~~ 57 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR------GSGSCP--ECDTPLRKNN 57 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC------CCCCCC--CCCCccchhh
Confidence 3689999986533221 222279999999999999742 346899 7998777654
No 26
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=0.00016 Score=72.16 Aligned_cols=55 Identities=20% Similarity=0.636 Sum_probs=44.5
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhh
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNI 171 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 171 (292)
....|++|.+-. .+.+ +..|+|.||..|++..+.. ..-+|| .|+..+++.+++.+
T Consensus 642 ~~LkCs~Cn~R~--Kd~v-I~kC~H~FC~~Cvq~r~et------RqRKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTRW--KDAV-ITKCGHVFCEECVQTRYET------RQRKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCch--hhHH-HHhcchHHHHHHHHHHHHH------hcCCCC--CCCCCCCccccccc
Confidence 479999999532 3333 3479999999999999997 457999 89999999988765
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.03 E-value=0.00041 Score=65.49 Aligned_cols=47 Identities=28% Similarity=0.709 Sum_probs=36.5
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
.+.|+||++.+... + ++.|||.||..|+..|+.. ...|| .|...+..
T Consensus 26 ~l~C~IC~d~~~~P--v-itpCgH~FCs~CI~~~l~~-------~~~CP--~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFDVP--V-LTSCSHTFCSLCIRRCLSN-------QPKCP--LCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhhCc--c-CCCCCCchhHHHHHHHHhC-------CCCCC--CCCCcccc
Confidence 69999999976533 2 4589999999999999863 24899 68876543
No 28
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.00056 Score=63.16 Aligned_cols=46 Identities=33% Similarity=0.754 Sum_probs=40.5
Q ss_pred cccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
.+|.||+|++...+.+.+++|.|.|...|+..||.. .+-.|| .|+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~------~r~~CP--vCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQ------TRTFCP--VCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhh------cCccCC--CCCC
Confidence 799999999999888888999999999999999986 456799 4664
No 29
>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=96.94 E-value=0.00096 Score=48.02 Aligned_cols=42 Identities=24% Similarity=0.548 Sum_probs=30.1
Q ss_pred cccccccccCCC----------CCceeecCCCCccchhhHHHHHHHHHhcCccccCCCC
Q 048441 108 FVCEICVESKSP----------NESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPV 156 (292)
Q Consensus 108 ~~C~IC~~~~~~----------~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 156 (292)
-.|.||++++.. .-.+....|||.|...||.+|++. .-.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-------~~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-------NNTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-------SSB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-------CCcCCC
Confidence 459999998822 123344589999999999999973 348983
No 30
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.90 E-value=0.00039 Score=62.39 Aligned_cols=43 Identities=26% Similarity=0.788 Sum_probs=36.6
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
..+.|+||++.+... .++.|+|.||..|+..++. ..+.|| .|+
T Consensus 12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCR 54 (386)
T ss_pred ccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccC
Confidence 479999999988765 4568999999999999998 458999 677
No 31
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=96.82 E-value=0.0015 Score=45.27 Aligned_cols=50 Identities=28% Similarity=0.634 Sum_probs=34.1
Q ss_pred HHHhcCccccCCCCCCCCCCCCHHH--HHhhCC---CCceeccCCCCCccCCCCc
Q 048441 143 SKLQESITTIGCPVTGCQGVLEPEY--CRNILP---QQVMFCAKCKVPWHTDMKC 192 (292)
Q Consensus 143 ~~i~~~~~~i~CP~~~C~~~l~~~~--i~~~l~---~~~~~C~~C~~~~H~~~~C 192 (292)
..|..+....+||.++|...+..+. -...+. -...||+.|+.+||.+++|
T Consensus 10 ~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 10 SYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred HHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 3444445678999999998776542 111111 1239999999999999887
No 32
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.75 E-value=0.00064 Score=61.79 Aligned_cols=50 Identities=30% Similarity=0.643 Sum_probs=39.9
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEY 167 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 167 (292)
...-|.||++-+.... +.+|+|.||.=||+.|+. ....|| .|...+...+
T Consensus 22 ~lLRC~IC~eyf~ip~---itpCsHtfCSlCIR~~L~-------~~p~CP--~C~~~~~Es~ 71 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPM---ITPCSHTFCSLCIRKFLS-------YKPQCP--TCCVTVTESD 71 (442)
T ss_pred HHHHHhHHHHHhcCce---eccccchHHHHHHHHHhc-------cCCCCC--ceecccchhh
Confidence 3688999999886544 347999999999999998 668999 6876665443
No 33
>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=96.75 E-value=0.00041 Score=48.06 Aligned_cols=46 Identities=28% Similarity=0.652 Sum_probs=26.3
Q ss_pred cCccccCCCCCCCCCCCCHHHHHhh--CCC---CceeccCCCCCccCCCCc
Q 048441 147 ESITTIGCPVTGCQGVLEPEYCRNI--LPQ---QVMFCAKCKVPWHTDMKC 192 (292)
Q Consensus 147 ~~~~~i~CP~~~C~~~l~~~~i~~~--l~~---~~~~C~~C~~~~H~~~~C 192 (292)
.+....+||.++|+..+..+..... +.- ...||+.|+.+||.+++|
T Consensus 14 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 14 SDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred CCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 3345569999999988776544333 222 239999999999999887
No 34
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.69 E-value=0.0013 Score=44.91 Aligned_cols=47 Identities=28% Similarity=0.751 Sum_probs=31.3
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
.+.|||.+..+. +.+....|+|.|.++.+.+|| .....+.||..+|.
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 699999998764 445555899999999999999 23367999999985
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.46 E-value=0.0029 Score=55.87 Aligned_cols=54 Identities=22% Similarity=0.541 Sum_probs=40.7
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYC 168 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 168 (292)
...+.|.||++.... +..++|||.||-.|+...+..+ ..-.|| .|+..+.+..+
T Consensus 213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKK-----KYEFCP--LCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCC---cccccccchhhHHHHHHHHHhh-----ccccCc--hhhhhccchhh
Confidence 347889999986543 3456899999999999954332 345699 79998888776
No 36
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.10 E-value=0.00095 Score=46.27 Aligned_cols=48 Identities=25% Similarity=0.652 Sum_probs=23.1
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEY 167 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 167 (292)
..-|++|++.+... +.+..|.|.||..|++..+. -.|| .|.......+
T Consensus 7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD 54 (65)
T PF14835_consen 7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQD 54 (65)
T ss_dssp TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS
T ss_pred hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHH
Confidence 57899999976543 34458999999999988554 2499 5876554433
No 37
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.04 E-value=0.0035 Score=66.28 Aligned_cols=141 Identities=20% Similarity=0.423 Sum_probs=86.0
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcC---ccccCCCCCCCCCCCCHHHHHhhCCCC-------
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQES---ITTIGCPVTGCQGVLEPEYCRNILPQQ------- 175 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~~l~~~------- 175 (292)
..-.|.|||.+-........+.|+|.|-..|.+..++..-..- ...|.|| -|...+.---++.+|++-
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldPiKel~edV 3562 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDPIKELYEDV 3562 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHHHHHHHHHH
Confidence 3678999998765554445579999999999999998765442 2468999 698877643333333220
Q ss_pred -----------------c----------------------eeccCCCCCccCCC-CchhHHHhcccchhHHHHHHHH---
Q 048441 176 -----------------V----------------------MFCAKCKVPWHTDM-KCEDFQNLNENENDDIKLKKLA--- 212 (292)
Q Consensus 176 -----------------~----------------------~~C~~C~~~~H~~~-~C~~~~~~~~~~~~~~~~~~~~--- 212 (292)
. ..|.+|++.+-++- .|..... .++.--.+++
T Consensus 3563 ~~KA~MRLEYeGL~ks~AiT~P~~~FYNdPa~YAmnRY~Y~vC~KCrKAYFGGEaRCdAe~~-----~ddydP~ELiCG~ 3637 (3738)
T KOG1428|consen 3563 RRKALMRLEYEGLHKSEAITTPGVRFYNDPAGYAMNRYAYYVCYKCRKAYFGGEARCDAEAG-----GDDYDPRELICGA 3637 (3738)
T ss_pred HHHHhhhhhhccccccccccCCCceeccChhhhhhhhhhhhhhhhhhhhhcCchhhcchhcC-----CCCCCHHHhhhcc
Confidence 0 89999999887663 5643221 1111111222
Q ss_pred --HhCCeeecCCCCeeEEec--CCcCe---EEeccCcceeeccccCcc
Q 048441 213 --VEMKWKRCPNCGYYVEKF--RGCNI---IICRCGTSFHYYSRADLS 253 (292)
Q Consensus 213 --~~~~~k~CP~C~~~iek~--~GCnh---m~C~C~~~FC~~C~~~~~ 253 (292)
.-...+-||+-++-+-.. .-|-. ..|.=-+|||-.|...+.
T Consensus 3638 CSDvS~aQmCPkHGtdfLEYKCRyCCSvAVfFCFGTTHFCn~CHDDFQ 3685 (3738)
T KOG1428|consen 3638 CSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDFQ 3685 (3738)
T ss_pred ccccccceecccccchhhhhhhheeeeEeEEEEcccccccchhhhHHH
Confidence 123457888766654211 11111 344455889999976655
No 38
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.68 E-value=0.015 Score=51.73 Aligned_cols=52 Identities=29% Similarity=0.618 Sum_probs=38.9
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
+...+|++|-+.-.. ......|||.||--|+..-+... ..+.|| .|+....+
T Consensus 237 t~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp--~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWD-----ASFTCP--LCGENVEP 288 (298)
T ss_pred cCCceeeccCCCCCC--Ceeeccccceeehhhhhhhhcch-----hhcccC--ccCCCCcc
Confidence 458999999985433 33444699999999999877643 458999 68877664
No 39
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.32 E-value=0.015 Score=41.49 Aligned_cols=57 Identities=18% Similarity=0.345 Sum_probs=26.0
Q ss_pred CcccccccccCC-CCCce--ee--cCCCCccchhhHHHHHHHHHhcCc----cccCCCCCCCCCCCCH
Q 048441 107 SFVCEICVESKS-PNESF--RI--KGCSHSYCTDCIIKYVASKLQESI----TTIGCPVTGCQGVLEP 165 (292)
Q Consensus 107 ~~~C~IC~~~~~-~~~~~--~~--~~CgH~fC~~Cl~~~i~~~i~~~~----~~i~CP~~~C~~~l~~ 165 (292)
...|.||+.... ..... .. ..|++.|...||.+|+...-.... ..-.|| .|...|..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 478999998765 22221 12 378899999999999987654321 223699 68876643
No 40
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.00 E-value=0.02 Score=53.17 Aligned_cols=56 Identities=30% Similarity=0.603 Sum_probs=40.3
Q ss_pred CCCcccccccccCCCCC-----ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCC
Q 048441 105 DPSFVCEICVESKSPNE-----SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGV 162 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~-----~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 162 (292)
....+|.||++.+.... .-++..|.|.||..|++.|=...-......-.|| .|+..
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CRv~ 219 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCRVP 219 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--cccCc
Confidence 45899999999875443 3334679999999999999865433334556888 57643
No 41
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.99 E-value=0.0085 Score=57.63 Aligned_cols=54 Identities=26% Similarity=0.683 Sum_probs=41.8
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPE 166 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 166 (292)
....|.+|-++-. +.+ ...|.|.||+-|++.|+......+ .+.|| .|...|+.+
T Consensus 535 ~~~~C~lc~d~ae--d~i-~s~ChH~FCrlCi~eyv~~f~~~~--nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 535 GEVECGLCHDPAE--DYI-ESSCHHKFCRLCIKEYVESFMENN--NVTCP--VCHIGLSID 588 (791)
T ss_pred CceeecccCChhh--hhH-hhhhhHHHHHHHHHHHHHhhhccc--CCCCc--ccccccccc
Confidence 3689999998532 322 348999999999999999877654 39999 788777654
No 42
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.96 E-value=0.0032 Score=57.69 Aligned_cols=49 Identities=33% Similarity=0.714 Sum_probs=37.4
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
..+.|+||++-+....+ ...|.|.||.+||..-+.. ..-.|| +|++.+.
T Consensus 42 ~~v~c~icl~llk~tmt--tkeClhrfc~~ci~~a~r~------gn~ecp--tcRk~l~ 90 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMT--TKECLHRFCFDCIWKALRS------GNNECP--TCRKKLV 90 (381)
T ss_pred hhhccHHHHHHHHhhcc--cHHHHHHHHHHHHHHHHHh------cCCCCc--hHHhhcc
Confidence 36999999997655443 3489999999999888775 456798 7886554
No 43
>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=94.87 E-value=0.0077 Score=34.27 Aligned_cols=23 Identities=43% Similarity=1.034 Sum_probs=16.9
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
|.||.|+..|..+ ...| .|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5799999998653 4667 577776
No 44
>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=94.54 E-value=0.021 Score=40.97 Aligned_cols=49 Identities=18% Similarity=0.247 Sum_probs=33.6
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPE 166 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 166 (292)
.|.|+|+.+-+. +.+. +++||.|++.+|..|+.. ....|| .++..+...
T Consensus 4 ~f~CpIt~~lM~--dPVi-~~~G~tyer~~I~~~l~~------~~~~~P--~t~~~l~~~ 52 (73)
T PF04564_consen 4 EFLCPITGELMR--DPVI-LPSGHTYERSAIERWLEQ------NGGTDP--FTRQPLSES 52 (73)
T ss_dssp GGB-TTTSSB-S--SEEE-ETTSEEEEHHHHHHHHCT------TSSB-T--TT-SB-SGG
T ss_pred ccCCcCcCcHhh--Ccee-CCcCCEEcHHHHHHHHHc------CCCCCC--CCCCcCCcc
Confidence 589999998554 4343 489999999999999985 457888 566666653
No 45
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.47 E-value=0.035 Score=51.36 Aligned_cols=50 Identities=18% Similarity=0.480 Sum_probs=37.7
Q ss_pred CCcccccccccCCC-C---------CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSP-N---------ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~-~---------~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
....|.||+|+.-. + ....-++|||.+...|++.|++ ..-.|| -|+..+.
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-------RqQTCP--ICr~p~i 345 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-------RQQTCP--ICRRPVI 345 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-------hccCCC--cccCccc
Confidence 36899999998422 1 1223468999999999999999 457899 6887643
No 46
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.31 E-value=0.024 Score=54.24 Aligned_cols=51 Identities=22% Similarity=0.673 Sum_probs=38.9
Q ss_pred CcccccccccCCCC----C------c----eeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 107 SFVCEICVESKSPN----E------S----FRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 107 ~~~C~IC~~~~~~~----~------~----~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
...|.||+.+++.- + + ..+++|.|.|-+.|+.+|+.. ..+.|| .|+..|++
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~------ykl~CP--vCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT------YKLICP--VCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh------hcccCC--ccCCCCCC
Confidence 78999999987521 0 1 224589999999999999985 568999 67776653
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.11 E-value=0.031 Score=36.62 Aligned_cols=45 Identities=24% Similarity=0.633 Sum_probs=22.1
Q ss_pred cccccccCCCCC-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCC
Q 048441 110 CEICVESKSPNE-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGV 162 (292)
Q Consensus 110 C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 162 (292)
|++|.+++...+ .+.--.||+.+|+.||.+.++. ..-.|| +|+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~------~~g~CP--gCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN------EGGRCP--GCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS------S-SB-T--TT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc------cCCCCC--CCCCC
Confidence 789999885433 2333489999999999887762 346899 68754
No 48
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.70 E-value=0.033 Score=55.31 Aligned_cols=46 Identities=22% Similarity=0.611 Sum_probs=36.2
Q ss_pred CcccccccccCCCCCc--eeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNES--FRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~--~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
...|+||.|++....- ...+.|+|.|+..|++.|++. .-.|| .|+.
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-------~qtCP--~CR~ 338 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-------QQTCP--TCRT 338 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH-------hCcCC--cchh
Confidence 6899999998865321 345689999999999999995 46788 5665
No 49
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=93.53 E-value=0.036 Score=49.67 Aligned_cols=43 Identities=30% Similarity=0.635 Sum_probs=34.2
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
..-|-||-+-+...- .+.|||.||.=||+.|+. ....|| .|..
T Consensus 25 ~lrC~IC~~~i~ip~---~TtCgHtFCslCIR~hL~-------~qp~CP--~Cr~ 67 (391)
T COG5432 25 MLRCRICDCRISIPC---ETTCGHTFCSLCIRRHLG-------TQPFCP--VCRE 67 (391)
T ss_pred HHHhhhhhheeecce---ecccccchhHHHHHHHhc-------CCCCCc--cccc
Confidence 678999998765432 358999999999999998 567888 4654
No 50
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=93.26 E-value=0.021 Score=52.09 Aligned_cols=48 Identities=31% Similarity=0.820 Sum_probs=37.4
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
+-.+|.+|-.-+... .++..|-|.||+.||..|+.. ..+|| .|...+.
T Consensus 14 ~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~-------~~~CP--~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEE-------SKYCP--TCDIVIH 61 (331)
T ss_pred cceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHH-------hccCC--ccceecc
Confidence 368999999866533 345589999999999999995 57999 6775544
No 51
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.047 Score=51.19 Aligned_cols=43 Identities=23% Similarity=0.525 Sum_probs=37.4
Q ss_pred CeeecCC--CCeeEEecCCcCeEEe-ccCcceeeccccCccCCCCC
Q 048441 216 KWKRCPN--CGYYVEKFRGCNIIIC-RCGTSFHYYSRADLSELYPY 258 (292)
Q Consensus 216 ~~k~CP~--C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~~~y 258 (292)
....||+ |..++-...|+.-..| +|.+.||.+|...|++..++
T Consensus 272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~C 317 (445)
T KOG1814|consen 272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHGVSPC 317 (445)
T ss_pred ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcCCCcc
Confidence 4589998 9999966679999999 89999999999999875543
No 52
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.97 E-value=0.11 Score=48.86 Aligned_cols=55 Identities=25% Similarity=0.593 Sum_probs=41.0
Q ss_pred CcccccccccCCCC--CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHH
Q 048441 107 SFVCEICVESKSPN--ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYC 168 (292)
Q Consensus 107 ~~~C~IC~~~~~~~--~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 168 (292)
..+|+||++..... .....+.|||.|=.+|++.|+. ......|| .|..+-....+
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp--~c~~katkr~i 60 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCP--LCSGKATKRQI 60 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCc--ccCChhHHHHH
Confidence 57999999987543 2333469999999999999994 23678999 68876554443
No 53
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.46 E-value=0.082 Score=47.71 Aligned_cols=52 Identities=19% Similarity=0.365 Sum_probs=39.8
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEY 167 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 167 (292)
+..-+|+||+.+-... ..+.|+|.||.-|++..+.. ....|+ .|+..++..-
T Consensus 5 ~~~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~n------dk~~Ca--vCR~pids~i 56 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKN------DKKTCA--VCRFPIDSTI 56 (324)
T ss_pred ccCCcceeeeccCCcC---ccccccchhhhhhhcchhhc------CCCCCc--eecCCCCcch
Confidence 4478999999876543 24589999999999998874 445699 6998887643
No 54
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=92.28 E-value=0.094 Score=49.77 Aligned_cols=70 Identities=21% Similarity=0.536 Sum_probs=47.1
Q ss_pred CCCCcccccccccCCCCC-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhhC------CCCc
Q 048441 104 NDPSFVCEICVESKSPNE-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNIL------PQQV 176 (292)
Q Consensus 104 ~~~~~~C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l------~~~~ 176 (292)
.++.-+|+||++-+..+. .+....|.|.|--.|+..|.. ..|| .|+-...+.-+...+ ...+
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---------~scp--vcR~~q~p~~ve~~~c~~c~~~~~L 240 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---------SSCP--VCRYCQSPSVVESSLCLACGCTEDL 240 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc---------CcCh--hhhhhcCcchhhhhhhhhhcccccE
Confidence 367899999999876543 222347999999999999875 6899 577666553333221 2233
Q ss_pred eeccCCCC
Q 048441 177 MFCAKCKV 184 (292)
Q Consensus 177 ~~C~~C~~ 184 (292)
..|..|+.
T Consensus 241 wicliCg~ 248 (493)
T KOG0804|consen 241 WICLICGN 248 (493)
T ss_pred EEEEEccc
Confidence 77777764
No 55
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.92 E-value=0.048 Score=30.02 Aligned_cols=12 Identities=50% Similarity=1.027 Sum_probs=9.3
Q ss_pred ecCCCCeeEEec
Q 048441 219 RCPNCGYYVEKF 230 (292)
Q Consensus 219 ~CP~C~~~iek~ 230 (292)
.||+|+..|+..
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 489999988753
No 56
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.58 E-value=0.12 Score=50.10 Aligned_cols=41 Identities=22% Similarity=0.384 Sum_probs=34.9
Q ss_pred CCCCeeEEe-cCCcCeEEeccCcceeeccccCccCCCCCCCC
Q 048441 221 PNCGYYVEK-FRGCNIIICRCGTSFHYYSRADLSELYPYRPA 261 (292)
Q Consensus 221 P~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~~~~~y~~~ 261 (292)
|.|+..+.. .+.+..+.|.|++.|||.|+.+|+....+..+
T Consensus 164 ~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~ 205 (444)
T KOG1815|consen 164 PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGA 205 (444)
T ss_pred CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccch
Confidence 589999987 77899999999999999999999876654444
No 57
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.54 E-value=0.056 Score=30.63 Aligned_cols=23 Identities=30% Similarity=0.524 Sum_probs=16.3
Q ss_pred eecCCCCeeEEecCCcCeEEeccCcceeeccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRAD 251 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~ 251 (292)
+.||+|+..++.. ..||-.||.+
T Consensus 3 ~~Cp~Cg~~~~~~-----------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD-----------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc-----------cccChhhCCC
Confidence 5799999976553 5677777654
No 58
>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=91.25 E-value=0.033 Score=48.55 Aligned_cols=52 Identities=25% Similarity=0.668 Sum_probs=39.7
Q ss_pred CcccccccccCCCC-Cc-eee-cCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPN-ES-FRI-KGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 107 ~~~C~IC~~~~~~~-~~-~~~-~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
...||||-.+.-.. ++ +.+ ..|-|.+|-+|+.+.+.. .+..||.++|+.+|-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~------GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR------GPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC------CCCCCCCccHHHHHH
Confidence 45799999776432 22 222 459999999999999875 788999999997654
No 59
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.17 E-value=0.14 Score=33.78 Aligned_cols=27 Identities=33% Similarity=0.796 Sum_probs=21.0
Q ss_pred eecCCCCeeEEecCC--cCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRG--CNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~G--Cnhm~C-~C~~~F 244 (292)
+.||.|+.++...++ -+++.| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 369999999977653 468999 699764
No 60
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=90.74 E-value=0.11 Score=41.67 Aligned_cols=34 Identities=18% Similarity=0.568 Sum_probs=26.7
Q ss_pred CcccccccccCCC-CCceeecCCC------CccchhhHHHHH
Q 048441 107 SFVCEICVESKSP-NESFRIKGCS------HSYCTDCIIKYV 141 (292)
Q Consensus 107 ~~~C~IC~~~~~~-~~~~~~~~Cg------H~fC~~Cl~~~i 141 (292)
.++|.||++.+.. .-++.+ .|| |.||.+|+++|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHH
Confidence 6999999999877 334444 454 789999999994
No 61
>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=89.87 E-value=0.43 Score=31.37 Aligned_cols=41 Identities=15% Similarity=0.622 Sum_probs=28.7
Q ss_pred ccccccccCCCCCceeecCCC-----CccchhhHHHHHHHHHhcCccccCCC
Q 048441 109 VCEICVESKSPNESFRIKGCS-----HSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~Cg-----H~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
.|-||++.....+.+ +.+|. |.+-.+|+.+|+..+ ...+||
T Consensus 1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~-----~~~~C~ 46 (49)
T smart00744 1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINES-----GNKTCE 46 (49)
T ss_pred CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHc-----CCCcCC
Confidence 488999833333433 34674 889999999999864 234787
No 62
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=89.70 E-value=0.21 Score=45.14 Aligned_cols=41 Identities=24% Similarity=0.625 Sum_probs=36.3
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKL 145 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i 145 (292)
.+...|.||+.-+.....|+.+.|.|.|-..|+.+||...+
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 45799999999998888788889999999999999998654
No 63
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.53 E-value=0.087 Score=53.17 Aligned_cols=18 Identities=11% Similarity=0.292 Sum_probs=9.8
Q ss_pred CCCccchhhHHHHHHHHH
Q 048441 128 CSHSYCTDCIIKYVASKL 145 (292)
Q Consensus 128 CgH~fC~~Cl~~~i~~~i 145 (292)
|+|.+|..||..|....+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhHHHHHHHHHhh
Confidence 555555555555554433
No 64
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.44 E-value=0.26 Score=43.28 Aligned_cols=56 Identities=11% Similarity=0.258 Sum_probs=43.5
Q ss_pred CCcccccccccCCCCC-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHh
Q 048441 106 PSFVCEICVESKSPNE-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRN 170 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 170 (292)
..+.|+||-+++.... ...+.+|||+||.+|...+|. ..+.|| .|...+...+|-.
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~p--v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDP--VTDKPLKDRDIIG 276 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------cccccc--CCCCcCcccceEe
Confidence 5899999999886543 345679999999999999998 456777 5777777655543
No 65
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.40 E-value=0.42 Score=30.87 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=22.9
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcceee
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSFHY 246 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~FC~ 246 (292)
-+||+|+..++...+=..++| .||+.+=|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 579999999988765447899 69887655
No 66
>PHA00626 hypothetical protein
Probab=89.32 E-value=0.31 Score=32.77 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=20.6
Q ss_pred ecCCCCe-eEEecCCcCe----EEe-ccCcceee
Q 048441 219 RCPNCGY-YVEKFRGCNI----IIC-RCGTSFHY 246 (292)
Q Consensus 219 ~CP~C~~-~iek~~GCnh----m~C-~C~~~FC~ 246 (292)
.||+|+. -|.|.+-|+. -.| .||+.|=-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 5999999 4778775544 778 68887743
No 67
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=88.92 E-value=0.34 Score=49.47 Aligned_cols=54 Identities=28% Similarity=0.641 Sum_probs=42.9
Q ss_pred CCCcccccccccCCCC-CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 105 DPSFVCEICVESKSPN-ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~-~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
...++|.||++.+... .+.+...|-|+|-..||+.|..+.-..+....+|| .|.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--ccc
Confidence 3589999999988654 35666778999999999999998545556778898 455
No 68
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.74 E-value=0.63 Score=28.67 Aligned_cols=27 Identities=33% Similarity=0.785 Sum_probs=20.0
Q ss_pred eecCCCCeeEEecC-----CcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFR-----GCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~-----GCnhm~C-~C~~~F 244 (292)
-.||+|+......+ +=..++| +|++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57999998876542 3348899 899877
No 69
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=88.70 E-value=0.19 Score=45.02 Aligned_cols=37 Identities=30% Similarity=0.839 Sum_probs=30.7
Q ss_pred hCCeeecCCCCeeEEecC-CcCeEEe-ccCcceeecccc
Q 048441 214 EMKWKRCPNCGYYVEKFR-GCNIIIC-RCGTSFHYYSRA 250 (292)
Q Consensus 214 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~FC~~C~~ 250 (292)
+..|-+||.|+.++-+.+ +=|...| +|+|||=-.=.+
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~ 63 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARE 63 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccccCHHH
Confidence 568999999999998887 8899999 899998554433
No 70
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.62 E-value=0.38 Score=43.85 Aligned_cols=48 Identities=33% Similarity=0.691 Sum_probs=38.8
Q ss_pred CcccccccccCCCC---CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPN---ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGV 162 (292)
Q Consensus 107 ~~~C~IC~~~~~~~---~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 162 (292)
...|.||-+++... ....++.|||.+|..|+...+.. ..+.|| .|+..
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~------~~i~cp--fcR~~ 53 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN------SRILCP--FCRET 53 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC------ceeecc--CCCCc
Confidence 47899999988643 34556789999999999999875 678886 78876
No 71
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.32 E-value=0.3 Score=45.13 Aligned_cols=38 Identities=29% Similarity=0.640 Sum_probs=29.1
Q ss_pred CCCCCCcccccccccCCCCCceeecCCCCccchhhHHHHHH
Q 048441 102 HKNDPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVA 142 (292)
Q Consensus 102 ~~~~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~ 142 (292)
.|+.+.-.|+||+-- +...+| .+|+|.-|.+||.+++-
T Consensus 417 lp~sEd~lCpICyA~-pi~Avf--~PC~H~SC~~CI~qHlm 454 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG-PINAVF--APCSHRSCYGCITQHLM 454 (489)
T ss_pred CCCcccccCcceecc-cchhhc--cCCCCchHHHHHHHHHh
Confidence 455678899999963 333344 48999999999999985
No 72
>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=88.13 E-value=0.6 Score=28.67 Aligned_cols=26 Identities=31% Similarity=0.867 Sum_probs=18.3
Q ss_pred eecCCCCeeEEecC------CcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFR------GCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~------GCnhm~C-~C~~~F 244 (292)
-.||+|+..+.-.. | ..++| +|++.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 46899988765541 3 37888 788776
No 73
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=88.05 E-value=0.26 Score=41.95 Aligned_cols=34 Identities=29% Similarity=0.775 Sum_probs=26.5
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVA 142 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~ 142 (292)
-.|.|.||-.++.... +..|||.||..|...-+.
T Consensus 195 IPF~C~iCKkdy~spv---vt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 195 IPFLCGICKKDYESPV---VTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred Cceeehhchhhccchh---hhhcchhHHHHHHHHHhc
Confidence 4789999999876433 347999999999876554
No 74
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=88.00 E-value=0.13 Score=47.04 Aligned_cols=31 Identities=32% Similarity=0.958 Sum_probs=26.2
Q ss_pred hCCeeecCCCCeeEEecC-CcCeEEe-ccCcce
Q 048441 214 EMKWKRCPNCGYYVEKFR-GCNIIIC-RCGTSF 244 (292)
Q Consensus 214 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~F 244 (292)
+..|.+||+|+..+-+.+ .=|.++| +|+|||
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 446999999999997765 5678899 899998
No 75
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.94 E-value=0.41 Score=31.69 Aligned_cols=27 Identities=30% Similarity=0.757 Sum_probs=19.8
Q ss_pred eeecCCCCe-eEEecCCcCeEEe-ccCccee
Q 048441 217 WKRCPNCGY-YVEKFRGCNIIIC-RCGTSFH 245 (292)
Q Consensus 217 ~k~CP~C~~-~iek~~GCnhm~C-~C~~~FC 245 (292)
.+.||+|+. .+.... +.++| +||+.+-
T Consensus 20 ~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL--DRWHCGKCGYTEF 48 (50)
T ss_pred cCcCcCCCcchheccC--CcEECCCcCCEEe
Confidence 468999998 444333 68999 7998763
No 76
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=86.31 E-value=0.17 Score=46.16 Aligned_cols=33 Identities=27% Similarity=0.574 Sum_probs=26.6
Q ss_pred hCCeeecCCCCeeEEecC-CcCeEEe-ccCcceee
Q 048441 214 EMKWKRCPNCGYYVEKFR-GCNIIIC-RCGTSFHY 246 (292)
Q Consensus 214 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~FC~ 246 (292)
+..|.+||+|+..+-+.+ .=|..+| +|+|||=-
T Consensus 35 ~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 35 KHLWVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred CCCeeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 346999999999997765 5678899 79998743
No 77
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=86.24 E-value=0.24 Score=31.41 Aligned_cols=30 Identities=27% Similarity=0.466 Sum_probs=21.6
Q ss_pred cCCCCeeEEecCCcCeEEeccCcceeeccccCccC
Q 048441 220 CPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSE 254 (292)
Q Consensus 220 CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 254 (292)
||-|.-.+. +-++=.|||.||..|+..|..
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~~~ 30 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERLWK 30 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHHHC
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHHHH
Confidence 566666665 347778999999999998764
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.95 E-value=0.87 Score=27.88 Aligned_cols=27 Identities=33% Similarity=0.694 Sum_probs=19.9
Q ss_pred eecCCCCeeEEecC-----CcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFR-----GCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~-----GCnhm~C-~C~~~F 244 (292)
-.||+|+...+-.+ +=..++| +|++.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 47999998886652 2347889 798877
No 79
>PHA03096 p28-like protein; Provisional
Probab=85.79 E-value=0.4 Score=43.57 Aligned_cols=53 Identities=19% Similarity=0.315 Sum_probs=36.3
Q ss_pred cccccccccCCCC----C-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 108 FVCEICVESKSPN----E-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 108 ~~C~IC~~~~~~~----~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
..|.||++.+... . .-.+..|.|.||..|++.|..+..... ..-.|| .|...+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e-~~~~c~--~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKE-TEPENR--RLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcc-cCcccc--chhhHH
Confidence 7899999977532 1 223468999999999999999876432 333444 455443
No 80
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=85.74 E-value=0.2 Score=45.64 Aligned_cols=32 Identities=28% Similarity=0.816 Sum_probs=25.6
Q ss_pred hCCeeecCCCCeeEEecC-CcCeEEe-ccCccee
Q 048441 214 EMKWKRCPNCGYYVEKFR-GCNIIIC-RCGTSFH 245 (292)
Q Consensus 214 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~FC 245 (292)
+..|.+||+|+..+-+.+ .=|.+.| +|+|||=
T Consensus 23 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 23 EGVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CCCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 346999999999997764 4567899 7999864
No 81
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=85.58 E-value=1.1 Score=41.08 Aligned_cols=46 Identities=28% Similarity=0.655 Sum_probs=35.0
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
...|+||+.....+-... .=|-+||-.|+-.|+. ..-.||..+|..
T Consensus 300 ~~~CpvClk~r~Nptvl~--vSGyVfCY~Ci~~Yv~-------~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKKRQNPTVLE--VSGYVFCYPCIFSYVV-------NYGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhccCCCceEE--ecceEEeHHHHHHHHH-------hcCCCCccCCcc
Confidence 689999998765444333 3689999999999998 346899766654
No 82
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=85.46 E-value=0.59 Score=44.52 Aligned_cols=37 Identities=22% Similarity=0.770 Sum_probs=29.2
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVAS 143 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~ 143 (292)
.+...|++|...+.... ....|||.||..|+..+...
T Consensus 19 ~~~l~C~~C~~vl~~p~--~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPV--QTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred cccccCccccccccCCC--CCCCCCCcccccccchhhcc
Confidence 44799999998765433 22479999999999999985
No 83
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=85.27 E-value=0.92 Score=33.47 Aligned_cols=32 Identities=28% Similarity=0.756 Sum_probs=24.7
Q ss_pred cCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 126 KGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 126 ~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
-.|+|.|..-||.+|+.++- ..-.|| -|+...
T Consensus 50 g~C~H~FH~hCI~kWl~~~~----~~~~CP--mCR~~w 81 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQS----SKGQCP--MCRQPW 81 (85)
T ss_pred ccCccHHHHHHHHHHHcccc----CCCCCC--CcCCee
Confidence 47999999999999999741 235898 577543
No 84
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=85.17 E-value=0.38 Score=42.20 Aligned_cols=46 Identities=24% Similarity=0.655 Sum_probs=34.8
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
.+.|-.|+---. ...|.++.|+|+||..|...-.. -.|| .|+..+.
T Consensus 3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~---------~~C~--lCkk~ir 48 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSP---------DVCP--LCKKSIR 48 (233)
T ss_pred eEEeccccccCC-CCceeeeechhhhhhhhcccCCc---------cccc--cccceee
Confidence 478998987655 66677889999999999875442 1888 6886643
No 85
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.02 E-value=0.44 Score=48.24 Aligned_cols=34 Identities=24% Similarity=0.509 Sum_probs=25.4
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcc------eeeccccCccCC
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTS------FHYYSRADLSEL 255 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~------FC~~C~~~~~~~ 255 (292)
+.|.||+|+..+. +..| .||+. ||-.||.+....
T Consensus 14 ~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 14 NNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETGTI 54 (645)
T ss_pred CCccccccCCCCC------CCcCCCCCCCCCcccccccccCCcccch
Confidence 4577888888773 3568 78866 999999886643
No 86
>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=84.57 E-value=0.77 Score=26.99 Aligned_cols=25 Identities=32% Similarity=0.941 Sum_probs=13.4
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
.||+|+....-.+|. .|.| .|+++|
T Consensus 4 ~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCcceeccCC-EEeCCcccccC
Confidence 699999998887774 5778 688876
No 87
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.42 E-value=0.76 Score=41.25 Aligned_cols=69 Identities=17% Similarity=0.350 Sum_probs=47.2
Q ss_pred CCCcccccccccCCCCCceeec-CCCCccchhhHHHHHHHHHhcCccccCCCC-CCCC---CCCCH----HHHHhhCCCC
Q 048441 105 DPSFVCEICVESKSPNESFRIK-GCSHSYCTDCIIKYVASKLQESITTIGCPV-TGCQ---GVLEP----EYCRNILPQQ 175 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~-~~C~---~~l~~----~~i~~~l~~~ 175 (292)
....-|.+|.+.++...++.+. -=.|.||.-|-++.|+.+-.. ..++||. ..|. ..++. .+|..+|..+
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~s--gevYCPSGdkCPLvgS~vPWAFMQGEIatILagd 343 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGAS--GEVYCPSGDKCPLVGSNVPWAFMQGEIATILAGD 343 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCC--CceeCCCCCcCcccCCcccHHHhhhhHHHHhccc
Confidence 3469999999988766655431 126999999999999976544 4799996 3565 23333 3556666544
No 88
>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=83.96 E-value=1.3 Score=26.15 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=17.7
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
.+.||.|+.+.+...+=-.|.| .|++.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4789999999999988788999 78875
No 89
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.65 E-value=1.2 Score=41.97 Aligned_cols=59 Identities=17% Similarity=0.338 Sum_probs=44.0
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHh
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRN 170 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 170 (292)
..|.|||=-+....++....+.|||+++++=+.+..+ +|...++|| =|.....+++.++
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq 391 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ 391 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence 4799999887776666666679999999987776654 444579999 5887777666554
No 90
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=82.56 E-value=0.55 Score=29.91 Aligned_cols=26 Identities=35% Similarity=0.967 Sum_probs=20.9
Q ss_pred CCeeecCCCCeeEEecCCcCeEEec---cCcce
Q 048441 215 MKWKRCPNCGYYVEKFRGCNIIICR---CGTSF 244 (292)
Q Consensus 215 ~~~k~CP~C~~~iek~~GCnhm~C~---C~~~F 244 (292)
.+.+.||+|++.- |+.-+.|+ |++.|
T Consensus 9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hccccCCcCcCcc----CcccccccCCccchhh
Confidence 4679999999876 88888883 87765
No 91
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=82.29 E-value=0.65 Score=42.71 Aligned_cols=51 Identities=22% Similarity=0.498 Sum_probs=35.8
Q ss_pred cccccccccCCCCC--ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHH
Q 048441 108 FVCEICVESKSPNE--SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEY 167 (292)
Q Consensus 108 ~~C~IC~~~~~~~~--~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 167 (292)
-.||.|++++...+ ++. .+||-.+|+=||...-+ . ..-+|| .|+...+.+.
T Consensus 15 d~cplcie~mditdknf~p-c~cgy~ic~fc~~~irq-~-----lngrcp--acrr~y~den 67 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFP-CPCGYQICQFCYNNIRQ-N-----LNGRCP--ACRRKYDDEN 67 (480)
T ss_pred ccCcccccccccccCCccc-CCcccHHHHHHHHHHHh-h-----ccCCCh--Hhhhhccccc
Confidence 34999999887543 444 48999999999865433 2 446899 6887655443
No 92
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.22 E-value=0.32 Score=32.57 Aligned_cols=46 Identities=26% Similarity=0.589 Sum_probs=31.8
Q ss_pred CcccccccccCCCCCceeecCCCCc-cchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHS-YCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
.-+|.||++-- .+.++. .|||. +|.+|-.+..+. ..-.|| -|+..+
T Consensus 7 ~dECTICye~p-vdsVlY--tCGHMCmCy~Cg~rl~~~------~~g~CP--iCRapi 53 (62)
T KOG4172|consen 7 SDECTICYEHP-VDSVLY--TCGHMCMCYACGLRLKKA------LHGCCP--ICRAPI 53 (62)
T ss_pred ccceeeeccCc-chHHHH--HcchHHhHHHHHHHHHHc------cCCcCc--chhhHH
Confidence 36899999853 333333 59995 899998887764 445788 577544
No 93
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=82.19 E-value=0.45 Score=48.43 Aligned_cols=55 Identities=29% Similarity=0.748 Sum_probs=40.0
Q ss_pred cccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhhCC
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNILP 173 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 173 (292)
+.|.||.+ ....+ +..|+|.||.+|+..+|... ....|| .|...+....+.....
T Consensus 455 ~~c~ic~~---~~~~~-it~c~h~~c~~c~~~~i~~~-----~~~~~~--~cr~~l~~~~l~s~~~ 509 (674)
T KOG1001|consen 455 HWCHICCD---LDSFF-ITRCGHDFCVECLKKSIQQS-----ENAPCP--LCRNVLKEKKLLSANP 509 (674)
T ss_pred cccccccc---cccce-eecccchHHHHHHHhccccc-----cCCCCc--HHHHHHHHHHHhhccc
Confidence 89999998 23333 45899999999999999753 222677 7998887766655433
No 94
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.54 E-value=2 Score=39.82 Aligned_cols=48 Identities=25% Similarity=0.608 Sum_probs=34.9
Q ss_pred CCCcccccccccCCCCCceeecCCCCc-cchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHS-YCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
+...+|.||+.+.. + ..+++|.|. .|.+|.+..-- ..=.|| -|+..+.
T Consensus 288 ~~gkeCVIClse~r--d-t~vLPCRHLCLCs~Ca~~Lr~-------q~n~CP--ICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESR--D-TVVLPCRHLCLCSGCAKSLRY-------QTNNCP--ICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCc--c-eEEecchhhehhHhHHHHHHH-------hhcCCC--ccccchH
Confidence 45799999998643 3 345699995 89999887762 234799 6887654
No 95
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=81.18 E-value=0.25 Score=44.45 Aligned_cols=34 Identities=15% Similarity=0.226 Sum_probs=23.9
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcceeeccccCccCCC
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTSFHYYSRADLSELY 256 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~~ 256 (292)
..+|--|-... .|-+| .|||-|||-|...|-...
T Consensus 239 ~~kC~LCLe~~------~~pSaTpCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 239 TRKCSLCLENR------SNPSATPCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCceEEEecCC------CCCCcCcCcchHHHHHHHHHHccc
Confidence 34555554443 25677 799999999999998644
No 96
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=80.89 E-value=0.95 Score=29.67 Aligned_cols=28 Identities=32% Similarity=0.594 Sum_probs=19.9
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
..+.||+|+.-+....-=+...| +||+.
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccce
Confidence 34789999976655544457888 88863
No 97
>PF04641 Rtf2: Rtf2 RING-finger
Probab=80.15 E-value=1.3 Score=39.68 Aligned_cols=60 Identities=13% Similarity=0.350 Sum_probs=45.2
Q ss_pred CCCcccccccccCCCC-CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHHhhCCC
Q 048441 105 DPSFVCEICVESKSPN-ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCRNILPQ 174 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~-~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 174 (292)
...|.|||...++... .++.+.+|||+|+..++...= ..-.|| .|+..+...+|-.|-+.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--------~~~~Cp--~c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--------KSKKCP--VCGKPFTEEDIIPLNPP 171 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--------cccccc--ccCCccccCCEEEecCC
Confidence 4579999999988543 456677999999999999882 123499 79999887766555553
No 98
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.13 E-value=0.55 Score=41.87 Aligned_cols=53 Identities=19% Similarity=0.439 Sum_probs=39.3
Q ss_pred CCcccccccccCCCCC-------ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 106 PSFVCEICVESKSPNE-------SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~-------~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
+...|.||-..+..+. -...++|+|+|-..|++.|.... ..-.|| -|...++.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG-----KkqtCP--YCKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG-----KKQTCP--YCKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec-----CCCCCc--hHHHHhhH
Confidence 4678999998775443 33456999999999999998642 346788 58877654
No 99
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.27 E-value=1.4 Score=41.87 Aligned_cols=46 Identities=28% Similarity=0.802 Sum_probs=33.7
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
.|.|.||+..+... + .++|||.||..|+.+-+. ....|| .|+..+.
T Consensus 84 ef~c~vc~~~l~~p--v-~tpcghs~c~~Cl~r~ld-------~~~~cp--~Cr~~l~ 129 (398)
T KOG4159|consen 84 EFECCVCSRALYPP--V-VTPCGHSFCLECLDRSLD-------QETECP--LCRDELV 129 (398)
T ss_pred hhhhhhhHhhcCCC--c-cccccccccHHHHHHHhc-------cCCCCc--ccccccc
Confidence 69999999866432 2 248999999999777333 456888 4876655
No 100
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=77.24 E-value=0.56 Score=40.01 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=25.4
Q ss_pred CCeeecCCCCeeEEecCCcCeEEeccCcceeeccccCcc
Q 048441 215 MKWKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLS 253 (292)
Q Consensus 215 ~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 253 (292)
.+.-.||-|.-.+.. -+.=.|||.|||.|...|-
T Consensus 16 ~~~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 16 GGDFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred CCccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 345789999887642 2334799999999998874
No 101
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=76.74 E-value=1.2 Score=34.58 Aligned_cols=26 Identities=38% Similarity=1.077 Sum_probs=18.2
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
+.||.|+..+-=-.- +-++| +||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 569999988743323 67888 677766
No 102
>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=76.35 E-value=2 Score=38.73 Aligned_cols=48 Identities=25% Similarity=0.659 Sum_probs=35.4
Q ss_pred ccccccccCCCC--CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 109 VCEICVESKSPN--ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 109 ~C~IC~~~~~~~--~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
.||+|-.+.-.. ..+.+..|+|..|.+|+-..+.. ..-.|| .|..+|-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~------g~~~Cp--eC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL------GPAQCP--ECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc------CCCCCC--cccchhh
Confidence 488888665322 22233489999999999998874 667899 8997764
No 103
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.11 E-value=1.4 Score=41.24 Aligned_cols=37 Identities=22% Similarity=0.618 Sum_probs=27.3
Q ss_pred CcccccccccCCCCC-ceeecCCCCccchhhHHHHHHH
Q 048441 107 SFVCEICVESKSPNE-SFRIKGCSHSYCTDCIIKYVAS 143 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i~~ 143 (292)
.-.|.||-+-++... +-.+..|||.|-..|+.+|++.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~ 41 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEG 41 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHcc
Confidence 467999965444432 3344469999999999999984
No 104
>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=74.80 E-value=1.6 Score=33.07 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=25.8
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCII 138 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~ 138 (292)
+...|++|...+.. ..|.+.+|||.|...|++
T Consensus 77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 35779999998866 456667999999999975
No 105
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=74.11 E-value=3.4 Score=24.99 Aligned_cols=26 Identities=35% Similarity=0.803 Sum_probs=13.9
Q ss_pred eecCCCCeeEEec----CCcCeEEe-ccCcc
Q 048441 218 KRCPNCGYYVEKF----RGCNIIIC-RCGTS 243 (292)
Q Consensus 218 k~CP~C~~~iek~----~GCnhm~C-~C~~~ 243 (292)
|.||+|+..++.. ++=..+.| .||+.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCE
Confidence 4699999999875 34555778 68753
No 106
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.08 E-value=2.4 Score=38.40 Aligned_cols=45 Identities=24% Similarity=0.736 Sum_probs=32.9
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
..-|+.|-.-+.. ......|+|.||.+||...+.. ..+.|| .|..
T Consensus 274 ~LkCplc~~Llrn--p~kT~cC~~~fc~eci~~al~d------sDf~Cp--nC~r 318 (427)
T COG5222 274 SLKCPLCHCLLRN--PMKTPCCGHTFCDECIGTALLD------SDFKCP--NCSR 318 (427)
T ss_pred cccCcchhhhhhC--cccCccccchHHHHHHhhhhhh------ccccCC--Cccc
Confidence 4889999874432 2233479999999999887764 568999 5764
No 107
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=73.81 E-value=1.2 Score=41.96 Aligned_cols=46 Identities=30% Similarity=0.816 Sum_probs=32.9
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
...|-||-+... -+.+.+|||..|..|+..|=.+ + ..-.||...|.
T Consensus 369 FeLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~s---d--~gq~CPFCRcE 414 (563)
T KOG1785|consen 369 FELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDS---D--EGQTCPFCRCE 414 (563)
T ss_pred HHHHHHhhccCC---CcccccccchHHHHHHHhhccc---C--CCCCCCceeeE
Confidence 567999998533 2456799999999999998653 1 24578854443
No 108
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=73.75 E-value=3 Score=31.47 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=22.7
Q ss_pred ecCCCCeeEEecC--CcCeEEe-ccCcceeec
Q 048441 219 RCPNCGYYVEKFR--GCNIIIC-RCGTSFHYY 247 (292)
Q Consensus 219 ~CP~C~~~iek~~--GCnhm~C-~C~~~FC~~ 247 (292)
-||.|+.++.-.+ -||.+.| -|.|.|=..
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 5999998865543 4999999 599988655
No 109
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.46 E-value=2.6 Score=43.29 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=30.0
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcc-----eeeccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTS-----FHYYSRAD 251 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 251 (292)
-.||+|.+++.-...=+.|.| .||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 479999999887777799999 79987 89999987
No 110
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.77 E-value=0.99 Score=39.40 Aligned_cols=17 Identities=18% Similarity=0.292 Sum_probs=14.6
Q ss_pred cCcceeeccccCccCCC
Q 048441 240 CGTSFHYYSRADLSELY 256 (292)
Q Consensus 240 C~~~FC~~C~~~~~~~~ 256 (292)
|||-|||-|+-+|-...
T Consensus 65 CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred cccceehHHHHHHHhhc
Confidence 99999999999987443
No 111
>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=72.41 E-value=9.3 Score=31.55 Aligned_cols=71 Identities=24% Similarity=0.569 Sum_probs=44.0
Q ss_pred CcccccccccCCCCCceee----cCCCCccc------hhhHHHHHHHHHhc------------------------Ccccc
Q 048441 107 SFVCEICVESKSPNESFRI----KGCSHSYC------TDCIIKYVASKLQE------------------------SITTI 152 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~----~~CgH~fC------~~Cl~~~i~~~i~~------------------------~~~~i 152 (292)
..+|+||+|--....+... -+|.-.+| .+||.+|-++.... ....+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L 81 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL 81 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence 4789999985332222211 24555555 47999988765422 12478
Q ss_pred CCCCCCCCCCCC----HHHHHhhCCCCceec
Q 048441 153 GCPVTGCQGVLE----PEYCRNILPQQVMFC 179 (292)
Q Consensus 153 ~CP~~~C~~~l~----~~~i~~~l~~~~~~C 179 (292)
.|| -|++.|. .+..+.+|..+...|
T Consensus 82 ~CP--LCRG~V~GWtvve~AR~~LN~K~RsC 110 (162)
T PF07800_consen 82 ACP--LCRGEVKGWTVVEPARRFLNAKKRSC 110 (162)
T ss_pred cCc--cccCceeceEEchHHHHHhccCCccC
Confidence 899 6887654 356888888765433
No 112
>PLN03086 PRLI-interacting factor K; Provisional
Probab=72.29 E-value=1.7 Score=43.15 Aligned_cols=31 Identities=35% Similarity=0.720 Sum_probs=18.0
Q ss_pred cccCCCCCCCCCCCCHHHHHhhCCCCceeccCCCCC
Q 048441 150 TTIGCPVTGCQGVLEPEYCRNILPQQVMFCAKCKVP 185 (292)
Q Consensus 150 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~C~~C~~~ 185 (292)
..+.||..+|+..+...++...+ .|..|+..
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~-----~C~~Cgk~ 462 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHV-----HCEKCGQA 462 (567)
T ss_pred cceeCCcccccceeeccccccCc-----cCCCCCCc
Confidence 45677766677766554444443 46666543
No 113
>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=71.50 E-value=2.6 Score=29.38 Aligned_cols=29 Identities=31% Similarity=0.770 Sum_probs=21.7
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
..+.||.|+....+...=..++| .||+.+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 45899999999998544456788 587653
No 114
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=71.29 E-value=4.3 Score=37.25 Aligned_cols=46 Identities=26% Similarity=0.586 Sum_probs=32.7
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
...++||||++.+...- ++. .=||..|..|-.. ..-+|| .|+..++
T Consensus 46 ~~lleCPvC~~~l~~Pi-~QC-~nGHlaCssC~~~----------~~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPI-FQC-DNGHLACSSCRTK----------VSNKCP--TCRLPIG 91 (299)
T ss_pred hhhccCchhhccCcccc-eec-CCCcEehhhhhhh----------hcccCC--ccccccc
Confidence 46899999999876532 321 3479999999862 345777 4777766
No 115
>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=71.13 E-value=4.1 Score=27.06 Aligned_cols=46 Identities=20% Similarity=0.463 Sum_probs=28.1
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPEYCR 169 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 169 (292)
.|.||.|...+.. .=|..++...-..+...+.|| -|...+..+.+.
T Consensus 2 ~f~CP~C~~~~~~---------------~~L~~H~~~~H~~~~~~v~CP--iC~~~~~~~l~~ 47 (54)
T PF05605_consen 2 SFTCPYCGKGFSE---------------SSLVEHCEDEHRSESKNVVCP--ICSSRVTDNLIR 47 (54)
T ss_pred CcCCCCCCCccCH---------------HHHHHHHHhHCcCCCCCccCC--CchhhhhhHHHH
Confidence 5888888874322 124555555544445678999 688766654443
No 116
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.07 E-value=2.1 Score=44.26 Aligned_cols=26 Identities=42% Similarity=1.030 Sum_probs=22.9
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCccee
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSFH 245 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~FC 245 (292)
..||.|+..+...+||. +| .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 36999999999999998 99 6998766
No 117
>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=70.36 E-value=4.7 Score=24.47 Aligned_cols=27 Identities=26% Similarity=0.645 Sum_probs=16.3
Q ss_pred eecCCCCeeEEecC-CcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFR-GCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~-GCnhm~C-~C~~~F 244 (292)
+-||.|+.++.-.+ +=..+.| .|++.+
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 46999998875543 2222388 688764
No 118
>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=70.11 E-value=3.5 Score=26.87 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=19.8
Q ss_pred CeeecC--CCCeeEEecCCcCeEEe-ccCc
Q 048441 216 KWKRCP--NCGYYVEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 216 ~~k~CP--~C~~~iek~~GCnhm~C-~C~~ 242 (292)
.-+.|| .|+.-|.-..--+..+| +|++
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 347899 99997766666688999 8986
No 119
>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=67.94 E-value=4.9 Score=25.39 Aligned_cols=22 Identities=41% Similarity=1.094 Sum_probs=16.7
Q ss_pred eecCCCCeeEEe-cCCcCeEEe-ccC
Q 048441 218 KRCPNCGYYVEK-FRGCNIIIC-RCG 241 (292)
Q Consensus 218 k~CP~C~~~iek-~~GCnhm~C-~C~ 241 (292)
..||.|+.++-+ ..| .+.| .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 689999999988 455 5677 553
No 120
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=66.74 E-value=4.2 Score=32.50 Aligned_cols=24 Identities=29% Similarity=0.505 Sum_probs=19.2
Q ss_pred eeecCCCCeeEEecCCcCeEEeccCcceeeccc
Q 048441 217 WKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSR 249 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~ 249 (292)
...||.|+.++.+..| ..||-+|+
T Consensus 28 ~~hCp~Cg~PLF~KdG---------~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDG---------EVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCC---------eEECCCCC
Confidence 3789999999987666 67777777
No 121
>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=66.64 E-value=6.6 Score=22.54 Aligned_cols=20 Identities=35% Similarity=0.677 Sum_probs=13.6
Q ss_pred ecCCCCeeEEecCCcCeEEe
Q 048441 219 RCPNCGYYVEKFRGCNIIIC 238 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C 238 (292)
.||.|+..+.+.+|=-.++|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999988777777
No 122
>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=66.53 E-value=3.1 Score=31.62 Aligned_cols=24 Identities=33% Similarity=0.934 Sum_probs=19.0
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
.||.|+.++...+| .+.| .|++.+
T Consensus 2 fC~~Cg~~l~~~~~--~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKNG--VYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCCC--eEECcCCCCcc
Confidence 69999999976554 7888 688764
No 123
>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=65.72 E-value=5.8 Score=28.12 Aligned_cols=35 Identities=26% Similarity=0.442 Sum_probs=22.5
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCc-----ceeeccccCccCC
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGT-----SFHYYSRADLSEL 255 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~-----~FC~~C~~~~~~~ 255 (292)
.||.|+..++..+ .+..| .|.. .+|-.|++++...
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~L 43 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEVL 43 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EEE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHHH
Confidence 5999999999888 68889 7885 4688898887643
No 124
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=65.33 E-value=5.9 Score=30.15 Aligned_cols=47 Identities=26% Similarity=0.458 Sum_probs=27.4
Q ss_pred CCeeecCCCCeeE---EecCCcCeEEe-ccCcceeeccccCccCCCCCCCC
Q 048441 215 MKWKRCPNCGYYV---EKFRGCNIIIC-RCGTSFHYYSRADLSELYPYRPA 261 (292)
Q Consensus 215 ~~~k~CP~C~~~i---ek~~GCnhm~C-~C~~~FC~~C~~~~~~~~~y~~~ 261 (292)
...-.||+|+... .+..|=-|+.| .||+.+=..-..-+..-+.|.-|
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~w 69 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKF 69 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHH
Confidence 3567899999432 23336668999 79887644333323333445444
No 125
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.03 E-value=2.8 Score=37.94 Aligned_cols=34 Identities=26% Similarity=0.578 Sum_probs=27.0
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVA 142 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~ 142 (292)
-.|-|-||-.++.... ++.|+|.||..|....+.
T Consensus 240 ~Pf~c~icr~~f~~pV---vt~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 240 LPFKCFICRKYFYRPV---VTKCGHYFCEVCALKPYQ 273 (313)
T ss_pred CCccccccccccccch---hhcCCceeehhhhccccc
Confidence 4688999999876433 247999999999887775
No 126
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=64.48 E-value=5.5 Score=29.44 Aligned_cols=29 Identities=34% Similarity=0.705 Sum_probs=22.9
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
.--.||.|+....+..+=---.| +||+.|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 34679999999888877777778 677766
No 127
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=63.79 E-value=11 Score=38.83 Aligned_cols=49 Identities=20% Similarity=0.440 Sum_probs=31.8
Q ss_pred cccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
-.|++|+..+.......-..|+|.||..||..|-.. .-.|| .|+..+..
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~-------aqTCP--iDR~EF~~ 172 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC-------AQTCP--VDRGEFGE 172 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh-------cccCc--hhhhhhhe
Confidence 345566554433332333479999999999999873 45788 57665543
No 128
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=63.03 E-value=1.4 Score=29.04 Aligned_cols=34 Identities=21% Similarity=0.487 Sum_probs=29.5
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKY 140 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~ 140 (292)
.++|..|-+..+..++.+..-||..-|..||+.-
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 6999999999988877666679999999999873
No 129
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=62.04 E-value=3.7 Score=37.62 Aligned_cols=42 Identities=24% Similarity=0.368 Sum_probs=34.9
Q ss_pred CCeeecC--CCCeeEEecCCcCeEEe-c-cCcceeeccccCccCCC
Q 048441 215 MKWKRCP--NCGYYVEKFRGCNIIIC-R-CGTSFHYYSRADLSELY 256 (292)
Q Consensus 215 ~~~k~CP--~C~~~iek~~GCnhm~C-~-C~~~FC~~C~~~~~~~~ 256 (292)
.+...|| .|+..+--..-|..++| . ||+.||-.|.+.++...
T Consensus 313 ~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~ge 358 (446)
T KOG0006|consen 313 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEGE 358 (446)
T ss_pred cCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhcccc
Confidence 4456776 89998888889999999 4 99999999999887544
No 130
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.03 E-value=2.5 Score=44.16 Aligned_cols=52 Identities=27% Similarity=0.579 Sum_probs=37.4
Q ss_pred CCcccccccccCC-CCC---ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKS-PNE---SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~-~~~---~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
.-.+|.||+.-+. .+. .-++..|.|.|...|+-.|+++. ..-.|| -|+..++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss-----~~s~CP--lCRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS-----ARSNCP--LCRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc-----CCCCCC--ccccccc
Confidence 3678999997553 111 11245699999999999999975 556899 6886654
No 131
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=62.01 E-value=9.6 Score=25.61 Aligned_cols=33 Identities=21% Similarity=0.487 Sum_probs=28.0
Q ss_pred CcccccccccCC-CCCceeecCCCCccchhhHHH
Q 048441 107 SFVCEICVESKS-PNESFRIKGCSHSYCTDCIIK 139 (292)
Q Consensus 107 ~~~C~IC~~~~~-~~~~~~~~~CgH~fC~~Cl~~ 139 (292)
..-|++|-+.+. .++++....||-.+-++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 578999999996 567777889999999999964
No 132
>PF12773 DZR: Double zinc ribbon
Probab=61.83 E-value=2.8 Score=27.22 Aligned_cols=12 Identities=42% Similarity=0.863 Sum_probs=6.8
Q ss_pred eeecCCCCeeEE
Q 048441 217 WKRCPNCGYYVE 228 (292)
Q Consensus 217 ~k~CP~C~~~ie 228 (292)
.+.||+|++.+.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 455666665555
No 133
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=60.60 E-value=11 Score=27.26 Aligned_cols=51 Identities=18% Similarity=0.401 Sum_probs=20.9
Q ss_pred CCCcccccccccCCC----CCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 105 DPSFVCEICVESKSP----NESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~----~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
.....|.||-+++-. ..++....|+-..|+.|+.--.+. ..-.|| .|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErke------g~q~Cp--qCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKE------GNQVCP--QCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHT------S-SB-T--TT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhc------Cccccc--ccCCCc
Confidence 346899999998742 233445678889999999765553 345788 576443
No 134
>PF15616 TerY-C: TerY-C metal binding domain
Probab=60.31 E-value=6.3 Score=31.56 Aligned_cols=26 Identities=31% Similarity=0.765 Sum_probs=18.5
Q ss_pred CeeecCCCCeeEEecCCcCeEEeccCcceeec
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIICRCGTSFHYY 247 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~ 247 (292)
+.--||.|+... ....|.||.-|||.
T Consensus 76 g~PgCP~CGn~~------~fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 76 GAPGCPHCGNQY------AFAVCGCGKLFCID 101 (131)
T ss_pred CCCCCCCCcChh------cEEEecCCCEEEeC
Confidence 346799999986 34566777777763
No 135
>PLN03086 PRLI-interacting factor K; Provisional
Probab=59.80 E-value=9.1 Score=38.21 Aligned_cols=29 Identities=31% Similarity=0.776 Sum_probs=19.6
Q ss_pred CeeecCC--CCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPN--CGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~--C~~~iek~~GCnhm~C-~C~~~F 244 (292)
....||+ |+..+.+...=+|..| .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 3456774 7777777777777777 676554
No 136
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=59.50 E-value=4.2 Score=27.38 Aligned_cols=46 Identities=24% Similarity=0.485 Sum_probs=29.4
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPE 166 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 166 (292)
...|-.|..... .-.+++|||.+|..||-.. ..--|| -|+..+...
T Consensus 7 ~~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~~---------rYngCP--fC~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVGT---KGTVLPCGHLICDNCFPGE---------RYNGCP--FCGTPFEFD 52 (55)
T ss_pred ceeEEEcccccc---ccccccccceeeccccChh---------hccCCC--CCCCcccCC
Confidence 355556654322 2234689999999998643 335688 688777653
No 137
>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=59.37 E-value=3.7 Score=28.56 Aligned_cols=36 Identities=19% Similarity=0.458 Sum_probs=19.2
Q ss_pred CCcccccccccCCCCC-ceeecCCCCccchhhHHHHH
Q 048441 106 PSFVCEICVESKSPNE-SFRIKGCSHSYCTDCIIKYV 141 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i 141 (292)
+...|.+|...|.... -.....||++||.+|....+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 4689999999885432 23456899999999986543
No 138
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=58.80 E-value=8.1 Score=26.85 Aligned_cols=28 Identities=29% Similarity=0.606 Sum_probs=19.5
Q ss_pred CeeecCCCCeeEEe---cCCcCeEEe-ccCcc
Q 048441 216 KWKRCPNCGYYVEK---FRGCNIIIC-RCGTS 243 (292)
Q Consensus 216 ~~k~CP~C~~~iek---~~GCnhm~C-~C~~~ 243 (292)
..|+||.|+..+.+ .+|=-.+.| .|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 46999999977544 356556677 57774
No 139
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=58.57 E-value=3.8 Score=38.96 Aligned_cols=37 Identities=24% Similarity=0.242 Sum_probs=25.0
Q ss_pred eeecCCCCeeEEecCCcC---eEEe--ccCcceeecc---ccCcc
Q 048441 217 WKRCPNCGYYVEKFRGCN---IIIC--RCGTSFHYYS---RADLS 253 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCn---hm~C--~C~~~FC~~C---~~~~~ 253 (292)
.-+|--|+.+|.-.+|+. .|.+ +=-|.=||.| +..+.
T Consensus 394 APrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 394 APRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred CcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCcccc
Confidence 457889999999999988 3445 3445556654 55555
No 140
>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=58.48 E-value=11 Score=23.78 Aligned_cols=24 Identities=33% Similarity=0.783 Sum_probs=12.5
Q ss_pred ecCCCCeeE-EecCCcCeEEe-ccCc
Q 048441 219 RCPNCGYYV-EKFRGCNIIIC-RCGT 242 (292)
Q Consensus 219 ~CP~C~~~i-ek~~GCnhm~C-~C~~ 242 (292)
.||.|+..- .-...=..++| .||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 588888753 33333344555 4543
No 141
>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=58.14 E-value=7 Score=30.10 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=19.6
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCccee
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSFH 245 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~FC 245 (292)
-.||+|+.-..-.+|= .+.| -|+|+|=
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCC-eeECcccccccc
Confidence 3699999988777774 4777 5776653
No 142
>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=57.17 E-value=4.8 Score=25.62 Aligned_cols=41 Identities=27% Similarity=0.657 Sum_probs=19.0
Q ss_pred cccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
|.+|-+-+.....-....|+=.+-..|+..|+... ..-+||
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~-----~~~~CP 41 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR-----SNPKCP 41 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT------SS-B-T
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC-----CCCCCc
Confidence 56676654433322223588889999999999753 222788
No 143
>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=56.81 E-value=8.4 Score=26.89 Aligned_cols=17 Identities=24% Similarity=0.804 Sum_probs=12.4
Q ss_pred ccchhhHHHHHHHHHhc
Q 048441 131 SYCTDCIIKYVASKLQE 147 (292)
Q Consensus 131 ~fC~~Cl~~~i~~~i~~ 147 (292)
-||+.|+..|+...-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999987654
No 144
>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=56.67 E-value=12 Score=25.65 Aligned_cols=27 Identities=26% Similarity=0.607 Sum_probs=19.6
Q ss_pred eecCCCCee----EEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYY----VEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~----iek~~GCnhm~C-~C~~~F 244 (292)
-.||+|+.+ +-+..|=.++.| .|||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 369999875 334567788999 798753
No 145
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=56.64 E-value=5.6 Score=31.55 Aligned_cols=26 Identities=23% Similarity=0.462 Sum_probs=17.6
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
+.||+|+..+---.- +-++| +||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 569999988743222 66788 677664
No 146
>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=56.46 E-value=4 Score=26.98 Aligned_cols=25 Identities=36% Similarity=0.623 Sum_probs=13.5
Q ss_pred eecCCCCeeEEecCC--cCeEEe-ccCc
Q 048441 218 KRCPNCGYYVEKFRG--CNIIIC-RCGT 242 (292)
Q Consensus 218 k~CP~C~~~iek~~G--Cnhm~C-~C~~ 242 (292)
-+|++|+..+-+.++ =-.|.| +|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 456666666655432 234666 5654
No 147
>PRK00420 hypothetical protein; Validated
Probab=56.43 E-value=7.4 Score=30.32 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=21.3
Q ss_pred eeecCCCCeeEEe-cCCcCeEEeccCcceeeccccCcc
Q 048441 217 WKRCPNCGYYVEK-FRGCNIIICRCGTSFHYYSRADLS 253 (292)
Q Consensus 217 ~k~CP~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~ 253 (292)
...||.|+.++.+ ..| ..||-.|+....
T Consensus 23 ~~~CP~Cg~pLf~lk~g---------~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG---------EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceecCCC---------ceECCCCCCeee
Confidence 4799999999987 455 667777777654
No 148
>PRK10220 hypothetical protein; Provisional
Probab=56.08 E-value=8.9 Score=29.58 Aligned_cols=27 Identities=22% Similarity=0.648 Sum_probs=19.3
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCccee
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSFH 245 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~FC 245 (292)
-.||+|..-..-.+|= .+.| -|+|+|=
T Consensus 4 P~CP~C~seytY~d~~-~~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICPECAHEWN 31 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECCcccCcCC
Confidence 4699999988777774 4677 5666653
No 149
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=55.45 E-value=16 Score=21.81 Aligned_cols=28 Identities=32% Similarity=0.685 Sum_probs=16.7
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
.+.|+.|+.....+.-=..+.| .|+..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 4678888877654322245666 566543
No 150
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=55.05 E-value=3.9 Score=38.52 Aligned_cols=48 Identities=29% Similarity=0.681 Sum_probs=36.6
Q ss_pred CcccccccccCCC-CCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSP-NESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~-~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
...|..|-+.+-. ++...-++|.|+|...|+..|+... ..-.|| .|++
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-----~~rsCP--~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-----GTRSCP--NCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-----CCCCCc--cHHH
Confidence 6899999987643 2334457999999999999999542 567899 6773
No 151
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=54.57 E-value=1.9 Score=39.25 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=17.0
Q ss_pred cccCCCCCCCCCCCCHHHHHhhC--CCCceeccCCCCCccCCC
Q 048441 150 TTIGCPVTGCQGVLEPEYCRNIL--PQQVMFCAKCKVPWHTDM 190 (292)
Q Consensus 150 ~~i~CP~~~C~~~l~~~~i~~~l--~~~~~~C~~C~~~~H~~~ 190 (292)
..-+|| .|++.-....++.-- .....+|..|...||...
T Consensus 171 ~~g~CP--vCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R 211 (290)
T PF04216_consen 171 QRGYCP--VCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR 211 (290)
T ss_dssp T-SS-T--TT---EEEEEEE------EEEEEETTT--EEE--T
T ss_pred cCCcCC--CCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC
Confidence 456999 688764432222221 234589999999998753
No 152
>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=54.44 E-value=14 Score=24.86 Aligned_cols=28 Identities=32% Similarity=0.857 Sum_probs=19.3
Q ss_pred eecCCCCeeEEecCCc--CeEEe-ccCccee
Q 048441 218 KRCPNCGYYVEKFRGC--NIIIC-RCGTSFH 245 (292)
Q Consensus 218 k~CP~C~~~iek~~GC--nhm~C-~C~~~FC 245 (292)
..||.|+..|+..+.= -.+.| .||..+=
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 3699999998876521 35677 5777653
No 153
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=54.20 E-value=10 Score=29.51 Aligned_cols=27 Identities=26% Similarity=0.723 Sum_probs=19.4
Q ss_pred eecCCCCeeEEec--CCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKF--RGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~--~GCnhm~C-~C~~~F 244 (292)
+.||+|+.++.-. ++=+-+.| +||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 6799999998662 12238888 688764
No 154
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.87 E-value=10 Score=40.05 Aligned_cols=33 Identities=27% Similarity=0.522 Sum_probs=26.1
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCc-----ceeeccccCccC
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGT-----SFHYYSRADLSE 254 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~-----~FC~~C~~~~~~ 254 (292)
..+.||.|+... ....| .||. .||-.|+.....
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEE 663 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCC
Confidence 458999999985 56789 6996 499999887653
No 155
>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=53.68 E-value=16 Score=24.70 Aligned_cols=46 Identities=33% Similarity=0.723 Sum_probs=33.0
Q ss_pred CcccccccccCCCCC-ceeecCCC--CccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 107 SFVCEICVESKSPNE-SFRIKGCS--HSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~-~~~~~~Cg--H~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
.-.|..|-.+++.+. -..+ |. ..||.+|....+. -.|| .|++.|..
T Consensus 5 rpnCE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l~---------~~CP--NCgGelv~ 53 (57)
T PF06906_consen 5 RPNCECCDKDLPPDSPEAYI--CSFECTFCADCAETMLN---------GVCP--NCGGELVR 53 (57)
T ss_pred CCCccccCCCCCCCCCcceE--EeEeCcccHHHHHHHhc---------CcCc--CCCCcccc
Confidence 467999998887654 2222 55 4799999988764 4799 69887754
No 156
>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=53.54 E-value=13 Score=26.47 Aligned_cols=27 Identities=26% Similarity=0.678 Sum_probs=19.7
Q ss_pred eecCCCCee----EEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYY----VEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~----iek~~GCnhm~C-~C~~~F 244 (292)
-.||+|+.+ +-+..|=.++.| .|||..
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 369999875 334467788999 799864
No 157
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=53.16 E-value=16 Score=23.56 Aligned_cols=33 Identities=24% Similarity=0.725 Sum_probs=22.0
Q ss_pred cccccccCCCCCceeecCCC--C---ccchhhHHHHHHH
Q 048441 110 CEICVESKSPNESFRIKGCS--H---SYCTDCIIKYVAS 143 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~Cg--H---~fC~~Cl~~~i~~ 143 (292)
|-||+++......+ +.+|. - ....+|+.+|+..
T Consensus 1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHh
Confidence 67999877655522 23554 3 6788999999997
No 158
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.76 E-value=4.3 Score=38.62 Aligned_cols=63 Identities=11% Similarity=0.172 Sum_probs=36.5
Q ss_pred eeecCCCCeeEEecC-----CcCeEEe-ccCcceeeccccCccCCCCCCCCCcccCCCCCCCChhhhhh
Q 048441 217 WKRCPNCGYYVEKFR-----GCNIIIC-RCGTSFHYYSRADLSELYPYRPASRQKGFRLKSRDPVRTLE 279 (292)
Q Consensus 217 ~k~CP~C~~~iek~~-----GCnhm~C-~C~~~FC~~C~~~~~~~~~y~~~~~~~~~~~~~~~~~~~l~ 279 (292)
+.+-|.|-..+.+.+ -=..-.| .|+..||..|+.+|+..-.+.-|..-+......+.++++|.
T Consensus 235 ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la 303 (384)
T KOG1812|consen 235 YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA 303 (384)
T ss_pred cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH
Confidence 334456766655443 1123457 79999999999999975444444333333333344445554
No 159
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=52.06 E-value=10 Score=23.66 Aligned_cols=13 Identities=46% Similarity=1.157 Sum_probs=9.6
Q ss_pred ecCCCCeeEEecC
Q 048441 219 RCPNCGYYVEKFR 231 (292)
Q Consensus 219 ~CP~C~~~iek~~ 231 (292)
.||+|+..++...
T Consensus 1 ~CP~C~~~l~~~~ 13 (41)
T PF13453_consen 1 KCPRCGTELEPVR 13 (41)
T ss_pred CcCCCCcccceEE
Confidence 4899998776553
No 160
>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=51.86 E-value=11 Score=37.29 Aligned_cols=34 Identities=21% Similarity=0.439 Sum_probs=26.7
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcc-----eeeccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTS-----FHYYSRAD 251 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 251 (292)
-+||+|.+.+.-...=+.+.| .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 469999988865545568999 79976 69999874
No 161
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.53 E-value=6.2 Score=32.66 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=19.9
Q ss_pred CCcccccccccCCCCCceeecCCCCccc
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYC 133 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC 133 (292)
.+.+|.||+|++...+.+.-++|-.+|-
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEee
Confidence 3678888888887777666667765553
No 162
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.26 E-value=15 Score=23.47 Aligned_cols=24 Identities=29% Similarity=0.703 Sum_probs=14.2
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
.|..|+..++...+ .-+.| .||+.
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCce
Confidence 46666666665543 45666 46654
No 163
>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=51.15 E-value=8.2 Score=25.63 Aligned_cols=16 Identities=31% Similarity=0.995 Sum_probs=8.5
Q ss_pred ceeecCCCCccchhhH
Q 048441 122 SFRIKGCSHSYCTDCI 137 (292)
Q Consensus 122 ~~~~~~CgH~fC~~Cl 137 (292)
.+....|++.||.+|=
T Consensus 21 ~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EE--TTTT--B-HHHH
T ss_pred eEECCCCCCccccCcC
Confidence 4556789999999993
No 164
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=50.96 E-value=14 Score=29.64 Aligned_cols=53 Identities=21% Similarity=0.474 Sum_probs=39.5
Q ss_pred CCcccccccccCCCCCceee-cCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESFRI-KGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~-~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
..++|.||-|......+..- .-||-.+|..|....++..- ....|| .|...+.
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 37999999998665544332 35899999999999998643 667899 5876543
No 165
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=50.79 E-value=10 Score=34.36 Aligned_cols=46 Identities=26% Similarity=0.569 Sum_probs=35.9
Q ss_pred CcccccccccCCCC-CceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPN-ESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~-~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
.+.||||.+.+... ..+..+.|||..-..|++.++.. . ..|| -|..
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~------~-y~CP--~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE------G-YTCP--ICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc------C-CCCC--cccc
Confidence 56799999877543 23445789999999999999873 3 8999 6888
No 166
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=50.76 E-value=4.7 Score=29.74 Aligned_cols=35 Identities=20% Similarity=0.540 Sum_probs=29.0
Q ss_pred eecCCCCeeEEecCCcCeEEeccCcceeeccccCccCC
Q 048441 218 KRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSEL 255 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~ 255 (292)
..||.|+.+ -+.|--+...|+|.|-..|...|-..
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHcc
Confidence 458888886 45788888899999999999999864
No 167
>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=50.41 E-value=11 Score=24.96 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=9.1
Q ss_pred eecCCCCeeEE
Q 048441 218 KRCPNCGYYVE 228 (292)
Q Consensus 218 k~CP~C~~~ie 228 (292)
|+||.|+..-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 78999998765
No 168
>PRK11827 hypothetical protein; Provisional
Probab=50.34 E-value=13 Score=25.60 Aligned_cols=27 Identities=19% Similarity=0.242 Sum_probs=20.1
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
+-.||.|+..++-..+=+..+| .|+-.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 4679999999887766567888 56643
No 169
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=49.75 E-value=5 Score=33.44 Aligned_cols=12 Identities=33% Similarity=1.082 Sum_probs=10.9
Q ss_pred eeccCCCCCccC
Q 048441 177 MFCAKCKVPWHT 188 (292)
Q Consensus 177 ~~C~~C~~~~H~ 188 (292)
..|..|+..||.
T Consensus 125 FRC~~C~RawH~ 136 (175)
T PF15446_consen 125 FRCTSCHRAWHF 136 (175)
T ss_pred EecCCccceeeh
Confidence 789999999985
No 170
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.31 E-value=3.1 Score=37.13 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=24.8
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcceeeccccC-ccC
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTSFHYYSRAD-LSE 254 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~-~~~ 254 (292)
-.+|+-|-...+. -.| .|||-|||.|+-. |..
T Consensus 215 d~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~ 248 (271)
T COG5574 215 DYKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTK 248 (271)
T ss_pred ccceeeeecccCC------cccccccchhhHHHHHHHHHh
Confidence 3568888877753 567 6999999999888 764
No 171
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=49.12 E-value=5.1 Score=36.27 Aligned_cols=35 Identities=26% Similarity=0.556 Sum_probs=25.3
Q ss_pred eecCCCCeeEEecCCcCeEEe--ccCcceeeccccCccCCCCCC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC--RCGTSFHYYSRADLSELYPYR 259 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C--~C~~~FC~~C~~~~~~~~~y~ 259 (292)
-+|--|+-.|. +-| .|||.||++|-+..-+.+++-
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~qp~C 62 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQPFC 62 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCCCCC
Confidence 46777777774 678 499999999987765555443
No 172
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=48.15 E-value=14 Score=37.86 Aligned_cols=47 Identities=28% Similarity=0.661 Sum_probs=35.4
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
...+.|.||.-.+...-.+ +..|+|+.-.+|++.|++. .=.||. +|+
T Consensus 1026 ~~~~~C~~C~l~V~gss~~-Cg~C~Hv~H~sc~~eWf~~-------gd~Cps-GCG 1072 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRGSSNF-CGTCGHVGHTSCMMEWFRT-------GDVCPS-GCG 1072 (1081)
T ss_pred cceeeeeeEeeEeeccchh-hccccccccHHHHHHHHhc-------CCcCCC-CCC
Confidence 4567888888776665544 4579999999999999984 238886 554
No 173
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=47.68 E-value=12 Score=40.68 Aligned_cols=30 Identities=33% Similarity=0.695 Sum_probs=20.4
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce-----eeccccCcc
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF-----HYYSRADLS 253 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F-----C~~C~~~~~ 253 (292)
++||+|+..+... +| .||.+. |-.|+....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccC
Confidence 7999999976432 77 577553 666666543
No 174
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=47.62 E-value=13 Score=25.32 Aligned_cols=22 Identities=36% Similarity=0.795 Sum_probs=15.8
Q ss_pred CCeeecCCCCeeEEecCCcCeEEe-ccC
Q 048441 215 MKWKRCPNCGYYVEKFRGCNIIIC-RCG 241 (292)
Q Consensus 215 ~~~k~CP~C~~~iek~~GCnhm~C-~C~ 241 (292)
.....||+|+.+... |-.| .||
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccCC-----eEECCCCC
Confidence 456789999999873 5555 455
No 175
>PHA02929 N1R/p28-like protein; Provisional
Probab=46.91 E-value=7.5 Score=34.46 Aligned_cols=39 Identities=23% Similarity=0.159 Sum_probs=28.3
Q ss_pred CeeecCCCCeeEEecCCcC---eEEeccCcceeeccccCccC
Q 048441 216 KWKRCPNCGYYVEKFRGCN---IIICRCGTSFHYYSRADLSE 254 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCn---hm~C~C~~~FC~~C~~~~~~ 254 (292)
....||-|...+.....-+ -+.-.|+|.||..|...|..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 4578999999876543222 23446999999999999875
No 176
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.90 E-value=15 Score=37.61 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=24.8
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcc----eeeccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTS----FHYYSRAD 251 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~----FC~~C~~~ 251 (292)
-+||+|...+....+=+.+.| .||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 489999988876555578999 79863 46667654
No 177
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=45.19 E-value=18 Score=28.00 Aligned_cols=13 Identities=31% Similarity=0.948 Sum_probs=11.4
Q ss_pred CeEEeccCcceee
Q 048441 234 NIIICRCGTSFHY 246 (292)
Q Consensus 234 nhm~C~C~~~FC~ 246 (292)
..+.|.|||.||-
T Consensus 23 k~vkc~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKCDCGHEFCD 35 (112)
T ss_pred ceeeccCCCeecC
Confidence 4789999999985
No 178
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=45.19 E-value=26 Score=33.03 Aligned_cols=35 Identities=26% Similarity=0.710 Sum_probs=22.9
Q ss_pred CCCccchhhHHHHHHHHHhcC------ccccCCCCCCCCCCCC
Q 048441 128 CSHSYCTDCIIKYVASKLQES------ITTIGCPVTGCQGVLE 164 (292)
Q Consensus 128 CgH~fC~~Cl~~~i~~~i~~~------~~~i~CP~~~C~~~l~ 164 (292)
|.-..|.+|+.+|+.++=.+. .....|| .|++.+-
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CP--tCRa~FC 351 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCP--TCRAKFC 351 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCC--CCcccce
Confidence 334468899999998764332 2345566 8987654
No 179
>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=44.91 E-value=17 Score=26.47 Aligned_cols=32 Identities=38% Similarity=0.758 Sum_probs=16.8
Q ss_pred CeeecCCCC----ee--EEecCCcCeEEe-ccCcceeec
Q 048441 216 KWKRCPNCG----YY--VEKFRGCNIIIC-RCGTSFHYY 247 (292)
Q Consensus 216 ~~k~CP~C~----~~--iek~~GCnhm~C-~C~~~FC~~ 247 (292)
..-.||.|+ +. |.+..|=-++.| .||..|=+.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 456899999 33 444567888999 687766443
No 180
>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 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=44.33 E-value=35 Score=22.34 Aligned_cols=47 Identities=23% Similarity=0.539 Sum_probs=24.0
Q ss_pred cccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
..|+|-+..+.. .+....|.|.-|.| +..||......+ ..+|| -|+.
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~--~W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTP--KWKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS-----B-T--TT--
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccC--CeECc--CCcC
Confidence 568888875543 34556899998876 677777766554 38899 5653
No 182
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=43.62 E-value=15 Score=24.67 Aligned_cols=22 Identities=36% Similarity=0.896 Sum_probs=15.4
Q ss_pred CCeeecCCCCeeEEecCCcCeEEe-ccC
Q 048441 215 MKWKRCPNCGYYVEKFRGCNIIIC-RCG 241 (292)
Q Consensus 215 ~~~k~CP~C~~~iek~~GCnhm~C-~C~ 241 (292)
.....||+|+.+.. .|-.| .||
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccC
Confidence 45578999999886 45555 455
No 183
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.14 E-value=19 Score=30.61 Aligned_cols=24 Identities=38% Similarity=1.013 Sum_probs=19.7
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
-+|++|+..+++ .| +.|+| +||+.
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCCCE
Confidence 589999999999 33 88999 78864
No 184
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.26 E-value=11 Score=34.14 Aligned_cols=30 Identities=30% Similarity=0.848 Sum_probs=21.5
Q ss_pred CcccccccccCCCCCceeecCCCCc-cchhhHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHS-YCTDCIIK 139 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~-fC~~Cl~~ 139 (292)
...|.||++. .-+.+ ++.|||. -|..|=+.
T Consensus 300 ~~LC~ICmDa--P~DCv-fLeCGHmVtCt~CGkr 330 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCV-FLECGHMVTCTKCGKR 330 (350)
T ss_pred HHHHHHHhcC--CcceE-EeecCcEEeehhhccc
Confidence 6889999984 34555 3599994 68877543
No 185
>PF14149 YhfH: YhfH-like protein
Probab=42.24 E-value=1.8 Score=26.64 Aligned_cols=28 Identities=32% Similarity=0.708 Sum_probs=20.9
Q ss_pred HhCCeeecCCCCeeEEecCCcCeEEe-cc
Q 048441 213 VEMKWKRCPNCGYYVEKFRGCNIIIC-RC 240 (292)
Q Consensus 213 ~~~~~k~CP~C~~~iek~~GCnhm~C-~C 240 (292)
+....|.|+.||..|+-..-|..+.| +|
T Consensus 9 rnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 9 RNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 33456899999999887767777777 55
No 186
>PHA02926 zinc finger-like protein; Provisional
Probab=42.23 E-value=9.6 Score=33.33 Aligned_cols=43 Identities=19% Similarity=0.110 Sum_probs=28.0
Q ss_pred HhCCeeecCCCCeeEEecC--CcCe--EEeccCcceeeccccCccCC
Q 048441 213 VEMKWKRCPNCGYYVEKFR--GCNI--IICRCGTSFHYYSRADLSEL 255 (292)
Q Consensus 213 ~~~~~k~CP~C~~~iek~~--GCnh--m~C~C~~~FC~~C~~~~~~~ 255 (292)
+...-+.|+-|-..+-+.. ++.. +.=.|+|.||+.|...|...
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence 3345588999997763321 1111 11148889999999999874
No 187
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.10 E-value=19 Score=26.81 Aligned_cols=17 Identities=12% Similarity=0.686 Sum_probs=14.6
Q ss_pred ccchhhHHHHHHHHHhc
Q 048441 131 SYCTDCIIKYVASKLQE 147 (292)
Q Consensus 131 ~fC~~Cl~~~i~~~i~~ 147 (292)
-||++|+..|.......
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999987654
No 188
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.09 E-value=6.1 Score=39.60 Aligned_cols=38 Identities=18% Similarity=0.463 Sum_probs=27.8
Q ss_pred CCcccccccccCCCCCcee-ecCCCCccchhhHHHHHHH
Q 048441 106 PSFVCEICVESKSPNESFR-IKGCSHSYCTDCIIKYVAS 143 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~-~~~CgH~fC~~Cl~~~i~~ 143 (292)
....|+||+..+....... .+.|||.+|.-|+......
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 3678999987765444322 2589999999999886653
No 189
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.84 E-value=18 Score=37.03 Aligned_cols=33 Identities=21% Similarity=0.429 Sum_probs=25.8
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCcc-----eeeccccC
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGTS-----FHYYSRAD 251 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 251 (292)
+||+|...+.-...=+.++| .||+. .|-.|+..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 69999988765444578999 79976 59999775
No 190
>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=41.60 E-value=15 Score=21.15 Aligned_cols=24 Identities=38% Similarity=1.081 Sum_probs=12.5
Q ss_pred eecCCCCeeEEecC--CcCeEEe-ccC
Q 048441 218 KRCPNCGYYVEKFR--GCNIIIC-RCG 241 (292)
Q Consensus 218 k~CP~C~~~iek~~--GCnhm~C-~C~ 241 (292)
++||.|+..+++.. |=....| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 57999999987653 4444555 453
No 191
>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=41.57 E-value=18 Score=22.11 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=5.8
Q ss_pred ecCCCCeeEEe
Q 048441 219 RCPNCGYYVEK 229 (292)
Q Consensus 219 ~CP~C~~~iek 229 (292)
+||.|+..++.
T Consensus 7 ~C~~Cg~~fe~ 17 (41)
T smart00834 7 RCEDCGHTFEV 17 (41)
T ss_pred EcCCCCCEEEE
Confidence 45555555443
No 192
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.45 E-value=23 Score=25.19 Aligned_cols=47 Identities=28% Similarity=0.640 Sum_probs=31.5
Q ss_pred CcccccccccCCCCCceeecCC--CCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCH
Q 048441 107 SFVCEICVESKSPNESFRIKGC--SHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEP 165 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~C--gH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 165 (292)
.-.|..|-.+++....-. +-| .|.||.+|...-+. -.|| .|++.|..
T Consensus 5 RPnCECCDrDLpp~s~dA-~ICtfEcTFCadCae~~l~---------g~CP--nCGGelv~ 53 (84)
T COG3813 5 RPNCECCDRDLPPDSTDA-RICTFECTFCADCAENRLH---------GLCP--NCGGELVA 53 (84)
T ss_pred cCCCcccCCCCCCCCCce-eEEEEeeehhHhHHHHhhc---------CcCC--CCCchhhc
Confidence 357888888876543211 124 48899999876654 4689 69887654
No 193
>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=41.09 E-value=56 Score=20.76 Aligned_cols=25 Identities=24% Similarity=0.602 Sum_probs=14.3
Q ss_pred eecCCCCee-EEecCCcCeEEe-ccCc
Q 048441 218 KRCPNCGYY-VEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 218 k~CP~C~~~-iek~~GCnhm~C-~C~~ 242 (292)
-.||+|+.. +-+..+=....| .|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 469999974 222233344566 4654
No 194
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.04 E-value=16 Score=38.03 Aligned_cols=40 Identities=30% Similarity=0.619 Sum_probs=32.0
Q ss_pred CCCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHH
Q 048441 105 DPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKL 145 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i 145 (292)
.+.-.|.+|.-.+.... |.+.+|||.|-.+|+...+....
T Consensus 815 ep~d~C~~C~~~ll~~p-F~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKP-FYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred cCccchHHhcchhhcCc-ceeeeccchHHHHHHHHHHHccc
Confidence 35689999998876554 55569999999999999987543
No 195
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=41.01 E-value=30 Score=20.36 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=20.5
Q ss_pred ecCCCCeeEEecCCcCeEEe-ccCc
Q 048441 219 RCPNCGYYVEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C-~C~~ 242 (292)
.|..|+..+.--.|=..+.| .|.+
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 58999999999899999999 6764
No 196
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=40.20 E-value=18 Score=27.62 Aligned_cols=26 Identities=27% Similarity=0.724 Sum_probs=21.5
Q ss_pred cCCCCccchhhHHHHHHHHHhcCccccCCCCCC
Q 048441 126 KGCSHSYCTDCIIKYVASKLQESITTIGCPVTG 158 (292)
Q Consensus 126 ~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~ 158 (292)
-.|.|.|-.-||.+||+ .+-.||...
T Consensus 79 G~CNHaFH~hCisrWlk-------tr~vCPLdn 104 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLK-------TRNVCPLDN 104 (114)
T ss_pred eecchHHHHHHHHHHHh-------hcCcCCCcC
Confidence 36999999999999999 457898533
No 197
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=39.11 E-value=27 Score=23.10 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=22.0
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHH
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKY 140 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~ 140 (292)
.|.||-..+..-..+.+ .=| .+|.+|+...
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 48999988765443443 566 8999999876
No 198
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=38.88 E-value=18 Score=32.81 Aligned_cols=35 Identities=29% Similarity=0.565 Sum_probs=16.8
Q ss_pred eecCCCCee-----EEecC--CcCeEEe-ccCcce------eeccccCc
Q 048441 218 KRCPNCGYY-----VEKFR--GCNIIIC-RCGTSF------HYYSRADL 252 (292)
Q Consensus 218 k~CP~C~~~-----iek~~--GCnhm~C-~C~~~F------C~~C~~~~ 252 (292)
..||-||.. |...+ |=.++.| .|+++| |-.||..-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 589999986 33334 8899999 799988 66787763
No 199
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.82 E-value=14 Score=37.56 Aligned_cols=33 Identities=27% Similarity=0.563 Sum_probs=20.5
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcc----eeeccccCccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTS----FHYYSRADLSE 254 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~----FC~~C~~~~~~ 254 (292)
+.||+|+..+.. +.-.| +||+. +|-.||.....
T Consensus 2 ~~Cp~Cg~~n~~----~akFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 2 LICPQCQFENPN----NNRFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred CcCCCCCCcCCC----CCccccccCCCCCCCcCCCCCCCCCc
Confidence 468888877643 23466 57654 47777766554
No 200
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=38.63 E-value=15 Score=24.70 Aligned_cols=14 Identities=36% Similarity=0.700 Sum_probs=11.2
Q ss_pred CCeeecCCCCeeEE
Q 048441 215 MKWKRCPNCGYYVE 228 (292)
Q Consensus 215 ~~~k~CP~C~~~ie 228 (292)
.....||.|+.+..
T Consensus 24 ~~l~~c~~cg~~~~ 37 (56)
T PF01783_consen 24 PNLVKCPNCGEPKL 37 (56)
T ss_dssp TSEEESSSSSSEES
T ss_pred cceeeeccCCCEec
Confidence 36688999998775
No 201
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=38.42 E-value=30 Score=31.85 Aligned_cols=55 Identities=18% Similarity=0.399 Sum_probs=36.9
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPE 166 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 166 (292)
+.|.||+=-+.-...+....+.|||++=+.=+... -++|...++|| -|...-..+
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~L----S~nG~~~FKCP--YCP~~~~~~ 389 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVL----SQNGVLSFKCP--YCPEMSKYE 389 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHH----hhcCcEEeeCC--CCCcchhhh
Confidence 47999986665555555556799999866544433 34677789999 577544433
No 202
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=38.07 E-value=43 Score=22.67 Aligned_cols=38 Identities=24% Similarity=0.466 Sum_probs=24.6
Q ss_pred CeeecCCCCeeEEecCCcCeEEeccCcceeeccccCccCCCCCCCCCcccCCCCCCCChh
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSELYPYRPASRQKGFRLKSRDPV 275 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~~~y~~~~~~~~~~~~~~~~~ 275 (292)
..+.||+|+++--+ ..|-.||.+... .|.-++++.|..
T Consensus 4 ~mr~C~~CgvYTLk-------------~~CP~CG~~t~~---------~~P~rfSp~D~y 41 (56)
T PRK13130 4 KIRKCPKCGVYTLK-------------EICPVCGGKTKN---------PHPPRFSPEDKY 41 (56)
T ss_pred cceECCCCCCEEcc-------------ccCcCCCCCCCC---------CCCCCCCCCCcc
Confidence 45889999998863 456677776553 334556666643
No 203
>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=37.96 E-value=18 Score=32.21 Aligned_cols=38 Identities=16% Similarity=0.521 Sum_probs=23.7
Q ss_pred ccccCCCCCCCCCCCCHHHHHh-hCCCC--------ceeccCCCCCc
Q 048441 149 ITTIGCPVTGCQGVLEPEYCRN-ILPQQ--------VMFCAKCKVPW 186 (292)
Q Consensus 149 ~~~i~CP~~~C~~~l~~~~i~~-~l~~~--------~~~C~~C~~~~ 186 (292)
..+|.||-+.|+..+.....+. -+... -+.|.+|...+
T Consensus 121 S~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred cccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 4689999999998776544321 11111 18888887654
No 204
>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=37.38 E-value=13 Score=22.17 Aligned_cols=22 Identities=45% Similarity=0.942 Sum_probs=9.7
Q ss_pred cCCCCeeEEecCCcCeEEe-ccCc
Q 048441 220 CPNCGYYVEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 220 CP~C~~~iek~~GCnhm~C-~C~~ 242 (292)
|..|+..++...+ .-+.| .||+
T Consensus 3 C~~Cg~~~~~~~~-~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPG-DPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTS-STSSBSSSS-
T ss_pred CCcCCCeeEcCCC-CcEECCcCCC
Confidence 4555555554333 34555 3554
No 205
>PF14353 CpXC: CpXC protein
Probab=37.28 E-value=39 Score=26.54 Aligned_cols=39 Identities=26% Similarity=0.623 Sum_probs=25.8
Q ss_pred cCCCCCCCCCCC------------CHHHHHhhCCCCc--eeccCCCCCccCCCCc
Q 048441 152 IGCPVTGCQGVL------------EPEYCRNILPQQV--MFCAKCKVPWHTDMKC 192 (292)
Q Consensus 152 i~CP~~~C~~~l------------~~~~i~~~l~~~~--~~C~~C~~~~H~~~~C 192 (292)
|.|| .|+..+ .++....+|..+. ..|..|+.......++
T Consensus 2 itCP--~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 2 ITCP--HCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred cCCC--CCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCE
Confidence 7898 687553 3455666776555 8999998876544443
No 206
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=37.01 E-value=34 Score=22.98 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=9.0
Q ss_pred CeeecCCCCeeE
Q 048441 216 KWKRCPNCGYYV 227 (292)
Q Consensus 216 ~~k~CP~C~~~i 227 (292)
..|+||-|+...
T Consensus 2 ~LkPCPFCG~~~ 13 (61)
T PF14354_consen 2 ELKPCPFCGSAD 13 (61)
T ss_pred CCcCCCCCCCcc
Confidence 358999998554
No 207
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=36.82 E-value=40 Score=18.88 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=18.7
Q ss_pred cCCCCeeEEecCCcCeEEe-ccCc
Q 048441 220 CPNCGYYVEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 220 CP~C~~~iek~~GCnhm~C-~C~~ 242 (292)
|-+|+.++.--.|=.++.| .|.+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 5678888888888889998 5764
No 208
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.80 E-value=30 Score=30.79 Aligned_cols=35 Identities=11% Similarity=0.237 Sum_probs=26.6
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASK 144 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~ 144 (292)
.--|..|+.+..... +..=||.||++||.+||..+
T Consensus 43 FdcCsLtLqPc~dPv---it~~GylfdrEaILe~ilaq 77 (303)
T KOG3039|consen 43 FDCCSLTLQPCRDPV---ITPDGYLFDREAILEYILAQ 77 (303)
T ss_pred cceeeeecccccCCc---cCCCCeeeeHHHHHHHHHHH
Confidence 466888888765433 23679999999999999765
No 209
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=36.08 E-value=23 Score=33.03 Aligned_cols=34 Identities=24% Similarity=0.674 Sum_probs=26.4
Q ss_pred CCCCcccccccccCCCCCceeecCCCCccchhhHHHH
Q 048441 104 NDPSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKY 140 (292)
Q Consensus 104 ~~~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~ 140 (292)
+++...|.||.+.+.- ..+++|+|.+|.-|-.+.
T Consensus 58 DEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~Rl 91 (493)
T COG5236 58 DEENMNCQICAGSTTY---SARYPCGHQICHACAVRL 91 (493)
T ss_pred ccccceeEEecCCceE---EEeccCCchHHHHHHHHH
Confidence 4568999999986643 235699999999997664
No 210
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=35.85 E-value=29 Score=29.35 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=20.9
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
-.|+.|+.++.+. +.+.|.| .|++..
T Consensus 150 a~~~~~g~~~~~~-~~~~~~c~~~~~~e 176 (189)
T PRK09521 150 AMCSRCRTPLVKK-GENELKCPNCGNIE 176 (189)
T ss_pred EEccccCCceEEC-CCCEEECCCCCCEE
Confidence 4799999999874 5599999 798653
No 211
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.22 E-value=44 Score=28.22 Aligned_cols=58 Identities=19% Similarity=0.441 Sum_probs=37.2
Q ss_pred CCCcccccccccCCC----CCceeecCCCCccchhhHHHHHHHHHhc----CccccCCCCCCCCCCCC
Q 048441 105 DPSFVCEICVESKSP----NESFRIKGCSHSYCTDCIIKYVASKLQE----SITTIGCPVTGCQGVLE 164 (292)
Q Consensus 105 ~~~~~C~IC~~~~~~----~~~~~~~~CgH~fC~~Cl~~~i~~~i~~----~~~~i~CP~~~C~~~l~ 164 (292)
.....|.||+-.... +.......||..|-.-|+..|++.-+.. ++..-.|| -|...+.
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pia 228 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIA 228 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCcce
Confidence 457889999853321 1222235799999999999999876643 23344788 5776553
No 212
>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=35.08 E-value=42 Score=26.63 Aligned_cols=35 Identities=31% Similarity=0.621 Sum_probs=26.2
Q ss_pred HHHHHHHhCCeeecCCCCee---EEecCCcCeEEe-ccCcc
Q 048441 207 KLKKLAVEMKWKRCPNCGYY---VEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 207 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 243 (292)
.+.+++. .+..||.|+.+ +.+.++=-.+.| .||..
T Consensus 85 ~L~~fI~--~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 85 LLDKFIK--EYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHC--HHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHH--HEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 4444554 46889999976 677788899999 69964
No 213
>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=34.97 E-value=37 Score=31.23 Aligned_cols=38 Identities=21% Similarity=0.451 Sum_probs=26.6
Q ss_pred cccCCCCCCCCCCCCHHHHHhhC---CCCceeccCCCCCccCC
Q 048441 150 TTIGCPVTGCQGVLEPEYCRNIL---PQQVMFCAKCKVPWHTD 189 (292)
Q Consensus 150 ~~i~CP~~~C~~~l~~~~i~~~l---~~~~~~C~~C~~~~H~~ 189 (292)
..-.|| .|++.-....++.-- ......|..|...||..
T Consensus 183 ~~~~CP--vCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~ 223 (305)
T TIGR01562 183 SRTLCP--ACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV 223 (305)
T ss_pred CCCcCC--CCCChhhhhhhcccCCCCCceEEEcCCCCCccccc
Confidence 355999 698776655555432 22348999999999975
No 214
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.86 E-value=25 Score=31.43 Aligned_cols=55 Identities=22% Similarity=0.541 Sum_probs=39.1
Q ss_pred CCcccccccccCCCCCce-eecCCC-----CccchhhHHHHHHHHHhc-CccccCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESF-RIKGCS-----HSYCTDCIIKYVASKLQE-SITTIGCPVTGCQGV 162 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~-~~~~Cg-----H~fC~~Cl~~~i~~~i~~-~~~~i~CP~~~C~~~ 162 (292)
....|=|||.+.+..... -+.+|. |+....|+..||.++-.. ....+.|| .|+..
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~--QCqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCP--QCQTE 80 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeech--hhcch
Confidence 368999999876544322 122443 789999999999987653 35789999 68854
No 215
>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=34.15 E-value=37 Score=22.24 Aligned_cols=29 Identities=28% Similarity=0.639 Sum_probs=19.9
Q ss_pred CeeecCCCCeeEEecC--------CcCeEEeccCcce
Q 048441 216 KWKRCPNCGYYVEKFR--------GCNIIICRCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~--------GCnhm~C~C~~~F 244 (292)
.+-.||+|+.-..-++ .=-+-+|+||..+
T Consensus 12 kY~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfni 48 (49)
T PF12677_consen 12 KYCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFNI 48 (49)
T ss_pred hhccCcccCCcEeecCcceEEEeccceeeeecccccc
Confidence 4678999998765553 3445578888653
No 216
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=34.15 E-value=20 Score=34.38 Aligned_cols=35 Identities=26% Similarity=0.587 Sum_probs=26.0
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVAS 143 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~ 143 (292)
+...|+||..-+. +. .++.|+|..|+.|.+..+.+
T Consensus 3 eelkc~vc~~f~~--ep-iil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYR--EP-IILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhcc--Cc-eEeecccHHHHHHHHhhccc
Confidence 3578999986443 22 34589999999999976553
No 217
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=34.06 E-value=25 Score=30.49 Aligned_cols=38 Identities=16% Similarity=0.453 Sum_probs=22.7
Q ss_pred ccccCCCCCCCCCCCCHHHHHh-hCCCCc------eeccCCCCCc
Q 048441 149 ITTIGCPVTGCQGVLEPEYCRN-ILPQQV------MFCAKCKVPW 186 (292)
Q Consensus 149 ~~~i~CP~~~C~~~l~~~~i~~-~l~~~~------~~C~~C~~~~ 186 (292)
..+|.||-+.|..++..+-+.. -+++.. +.|.+|+..+
T Consensus 136 SqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred cceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 3678899999988776542221 111111 7788887643
No 218
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.65 E-value=28 Score=37.88 Aligned_cols=11 Identities=9% Similarity=-0.073 Sum_probs=6.3
Q ss_pred eeeccccCccC
Q 048441 244 FHYYSRADLSE 254 (292)
Q Consensus 244 FC~~C~~~~~~ 254 (292)
+|-.|+.+...
T Consensus 711 ~CP~CGtplv~ 721 (1337)
T PRK14714 711 ECPRCDVELTP 721 (1337)
T ss_pred cCCCCCCcccc
Confidence 56666655543
No 219
>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=33.60 E-value=30 Score=22.74 Aligned_cols=35 Identities=14% Similarity=0.474 Sum_probs=24.8
Q ss_pred cccccccccCCCCC-ceeecCCCCccchhhHHHHHH
Q 048441 108 FVCEICVESKSPNE-SFRIKGCSHSYCTDCIIKYVA 142 (292)
Q Consensus 108 ~~C~IC~~~~~~~~-~~~~~~CgH~fC~~Cl~~~i~ 142 (292)
..|.+|-..+.... -.....||++||.+|....+.
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 56888877665422 233457999999999987765
No 220
>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=33.37 E-value=27 Score=22.37 Aligned_cols=46 Identities=20% Similarity=0.464 Sum_probs=31.1
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCC
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCP 155 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 155 (292)
.|.||........++....|+..|...|+.-......... ....||
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~-~~w~C~ 46 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPS-GDWYCP 46 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHS-SSBSSH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCC-CcEECc
Confidence 4788888666777787788998888888877665432211 145555
No 221
>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=33.15 E-value=32 Score=26.83 Aligned_cols=33 Identities=21% Similarity=0.408 Sum_probs=22.2
Q ss_pred CcccccccccCCC--CCceeecCCCCccchhhHHH
Q 048441 107 SFVCEICVESKSP--NESFRIKGCSHSYCTDCIIK 139 (292)
Q Consensus 107 ~~~C~IC~~~~~~--~~~~~~~~CgH~fC~~Cl~~ 139 (292)
...|.+|..++.. ........|.|.+|..|-..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 5689999987642 22345678999999998544
No 222
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.01 E-value=35 Score=30.97 Aligned_cols=29 Identities=24% Similarity=0.575 Sum_probs=24.9
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
..+-||+|+...+-..|=-.+.| .||+.+
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 45899999999999988888999 788765
No 223
>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=32.78 E-value=52 Score=22.42 Aligned_cols=32 Identities=16% Similarity=0.374 Sum_probs=21.8
Q ss_pred cccccccCCCCCceeecCCCCccchh----hHHHHHHH
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTD----CIIKYVAS 143 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~----Cl~~~i~~ 143 (292)
|..|... ..++...+.||+++|-+ ....+.+.
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 5667643 34566778999999997 77777764
No 224
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.73 E-value=23 Score=32.77 Aligned_cols=29 Identities=24% Similarity=0.749 Sum_probs=20.6
Q ss_pred cccccccCCCCCceeecCCCCccchhhHH
Q 048441 110 CEICVESKSPNESFRIKGCSHSYCTDCII 138 (292)
Q Consensus 110 C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~ 138 (292)
|=.|.++......+.+..|.+.||.+|=.
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv 361 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCDV 361 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccchH
Confidence 77776666666666667788888888843
No 225
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=32.39 E-value=73 Score=24.66 Aligned_cols=34 Identities=26% Similarity=0.625 Sum_probs=24.6
Q ss_pred HHHHHHHhCCeeecCCCCee---EEecCCcCeEEe-ccCc
Q 048441 207 KLKKLAVEMKWKRCPNCGYY---VEKFRGCNIIIC-RCGT 242 (292)
Q Consensus 207 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~ 242 (292)
.+.+++. .+..||.|+.+ ++|.++=-.+.| .||.
T Consensus 72 ~l~~yI~--~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 72 LLRRYIK--EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHH--hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 3444554 57899999976 666677677889 6886
No 226
>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=32.08 E-value=15 Score=38.17 Aligned_cols=33 Identities=27% Similarity=0.595 Sum_probs=0.0
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcc-----eeeccccCccC
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTS-----FHYYSRADLSE 254 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~~~ 254 (292)
..++||+|+.... ..+| .||.+ +|..|+.....
T Consensus 654 ~~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~ 692 (900)
T PF03833_consen 654 GRRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEE 692 (900)
T ss_dssp ---------------------------------------------
T ss_pred ecccCcccCCcch------hhcCcccCCccccceeccccccccCc
Confidence 4588999998864 4678 68866 78888877654
No 227
>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=32.08 E-value=33 Score=19.01 Aligned_cols=8 Identities=63% Similarity=1.323 Sum_probs=4.9
Q ss_pred eeecCCCC
Q 048441 217 WKRCPNCG 224 (292)
Q Consensus 217 ~k~CP~C~ 224 (292)
.-.||+|+
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34677775
No 228
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=31.84 E-value=18 Score=39.27 Aligned_cols=37 Identities=30% Similarity=0.716 Sum_probs=30.6
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASK 144 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~ 144 (292)
..+.|+||.+.+....++. .|||.+|..|...|...+
T Consensus 1152 ~~~~c~ic~dil~~~~~I~--~cgh~~c~~c~~~~l~~~ 1188 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIA--GCGHEPCCRCDELWLYAS 1188 (1394)
T ss_pred cccchHHHHHHHHhcCCee--eechhHhhhHHHHHHHHh
Confidence 4679999999887555554 599999999999999854
No 229
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=31.23 E-value=50 Score=26.46 Aligned_cols=26 Identities=27% Similarity=0.750 Sum_probs=16.3
Q ss_pred eeecC--CCCeeEEecCCcCeEEe-ccCcc
Q 048441 217 WKRCP--NCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 217 ~k~CP--~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
+..|| .|+..|... |=+..+| +|+..
T Consensus 18 Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 18 YPACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp EEE-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred ECCCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 47899 999998877 3345777 67654
No 230
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=31.11 E-value=24 Score=31.49 Aligned_cols=47 Identities=32% Similarity=0.487 Sum_probs=35.4
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQ 160 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 160 (292)
...|||=+.++..... -..|||+|=++=+..++.. ...+.||..+|.
T Consensus 176 s~rdPis~~~I~nPvi--SkkC~HvydrDsI~~~l~~-----~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVI--SKKCGHVYDRDSIMQILCD-----EITIRCPVLGCE 222 (262)
T ss_pred cccCchhhhhhhchhh--hcCcCcchhhhhHHHHhcc-----CceeecccccCC
Confidence 4678887766544332 2479999999998888863 357999999999
No 231
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=30.48 E-value=77 Score=25.60 Aligned_cols=35 Identities=26% Similarity=0.640 Sum_probs=24.8
Q ss_pred HHHHHHHhCCeeecCCCCee---EEecCCcCeEEe-ccCcc
Q 048441 207 KLKKLAVEMKWKRCPNCGYY---VEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 207 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 243 (292)
.+.+++. .+..||.|+.+ ++|.+.=..+.| .||+.
T Consensus 94 ~L~~yI~--~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 94 KIDRYVK--EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred HHHHHHH--hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3444554 57899999976 666666667889 68875
No 232
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=30.20 E-value=49 Score=29.58 Aligned_cols=29 Identities=17% Similarity=0.525 Sum_probs=22.2
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
..+.||.|+..++...|=..+.| .|+...
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEE
Confidence 46899999999877655567889 788543
No 233
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.15 E-value=38 Score=31.12 Aligned_cols=32 Identities=22% Similarity=0.561 Sum_probs=22.3
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKY 140 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~ 140 (292)
..-|.-|--.+..-- .+..|.|+||.+|-+..
T Consensus 90 VHfCd~Cd~PI~IYG--RmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYG--RMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcceeee--cccccchhhhhhhhhcC
Confidence 567888876554321 23489999999998754
No 234
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=29.91 E-value=26 Score=33.77 Aligned_cols=34 Identities=24% Similarity=0.538 Sum_probs=22.9
Q ss_pred ccCCCCCCCCCCCCHHHHH-hhCCCCceeccCCCC
Q 048441 151 TIGCPVTGCQGVLEPEYCR-NILPQQVMFCAKCKV 184 (292)
Q Consensus 151 ~i~CP~~~C~~~l~~~~i~-~~l~~~~~~C~~C~~ 184 (292)
..+|-+..|+..|+.+++. .+...+..||..|.-
T Consensus 97 ~~rCrN~aC~s~LP~ddc~C~iC~~~~gFC~~C~C 131 (446)
T PF07227_consen 97 YKRCRNLACRSQLPVDDCDCKICCSEPGFCRRCMC 131 (446)
T ss_pred HHhcCCHHhhccCCccccCcchhcCCCCccccCCc
Confidence 4578777888888777665 344555577777753
No 235
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.86 E-value=34 Score=22.50 Aligned_cols=19 Identities=37% Similarity=0.618 Sum_probs=8.0
Q ss_pred cCCCCeeEEecCCcCeEEe
Q 048441 220 CPNCGYYVEKFRGCNIIIC 238 (292)
Q Consensus 220 CP~C~~~iek~~GCnhm~C 238 (292)
|-.|+..++....=.-+.|
T Consensus 9 C~~Cg~~~~~~~~~~~irC 27 (49)
T COG1996 9 CARCGREVELDQETRGIRC 27 (49)
T ss_pred hhhcCCeeehhhccCceeC
Confidence 4444444443333333444
No 236
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=29.86 E-value=36 Score=27.98 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=17.6
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcc
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 243 (292)
+..||.|+..|...+. ....| +|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4789999999987654 34555 45443
No 237
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=29.85 E-value=84 Score=25.22 Aligned_cols=35 Identities=20% Similarity=0.561 Sum_probs=24.1
Q ss_pred HHHHHHHhCCeeecCCCCee---EEecCCcCeEEe-ccCcc
Q 048441 207 KLKKLAVEMKWKRCPNCGYY---VEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 207 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 243 (292)
.+.+++. .+..||.|+.+ +.|.+.=..+.| .||+.
T Consensus 89 ~L~~yI~--~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 89 RIEDYVR--KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHh--heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 3444454 57899999976 566655456789 68875
No 238
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.70 E-value=13 Score=34.74 Aligned_cols=43 Identities=21% Similarity=0.604 Sum_probs=27.9
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVL 163 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 163 (292)
..-.|.||.++... +...+|||.-| |..-+-. ...|| -|...+
T Consensus 304 ~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~~--------l~~CP--vCR~rI 346 (355)
T KOG1571|consen 304 QPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSKH--------LPQCP--VCRQRI 346 (355)
T ss_pred CCCceEEecCCccc---eeeecCCcEEE--chHHHhh--------CCCCc--hhHHHH
Confidence 46899999997654 33448999866 5544432 24598 576543
No 239
>PRK12496 hypothetical protein; Provisional
Probab=29.37 E-value=29 Score=28.87 Aligned_cols=31 Identities=13% Similarity=0.297 Sum_probs=21.1
Q ss_pred CCee-ecCCCCeeEEecCCcCeEEeccCcceeeccccCccC
Q 048441 215 MKWK-RCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSE 254 (292)
Q Consensus 215 ~~~k-~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 254 (292)
..|+ +|+.|+..+..+. ...||-.||.+...
T Consensus 124 ~~w~~~C~gC~~~~~~~~---------~~~~C~~CG~~~~r 155 (164)
T PRK12496 124 IKWRKVCKGCKKKYPEDY---------PDDVCEICGSPVKR 155 (164)
T ss_pred eeeeEECCCCCccccCCC---------CCCcCCCCCChhhh
Confidence 3565 5999998885431 03678888887754
No 240
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.27 E-value=53 Score=21.81 Aligned_cols=30 Identities=30% Similarity=0.768 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCCHHHHHhhCCC-CceeccCCCC
Q 048441 153 GCPVTGCQGVLEPEYCRNILPQ-QVMFCAKCKV 184 (292)
Q Consensus 153 ~CP~~~C~~~l~~~~i~~~l~~-~~~~C~~C~~ 184 (292)
.|- +|...|++..+..+... +..+|..|+.
T Consensus 24 ~C~--gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCS--GCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccC--CCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 676 79999999988888665 5689999875
No 241
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.17 E-value=55 Score=19.92 Aligned_cols=24 Identities=38% Similarity=0.837 Sum_probs=16.4
Q ss_pred eecCCCCeeEEec-CCcCeEEe-ccCcc
Q 048441 218 KRCPNCGYYVEKF-RGCNIIIC-RCGTS 243 (292)
Q Consensus 218 k~CP~C~~~iek~-~GCnhm~C-~C~~~ 243 (292)
.+|+.|+...-.. +| ..+| +||+.
T Consensus 9 ~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 4699999885443 45 6777 67764
No 242
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=27.73 E-value=60 Score=26.90 Aligned_cols=52 Identities=15% Similarity=0.402 Sum_probs=35.3
Q ss_pred CCcccccccccCCCCCceeecCCCC---ccchhhHHHHHHHHHhcCccccCCCCCCCCCCCCHH
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSH---SYCTDCIIKYVASKLQESITTIGCPVTGCQGVLEPE 166 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH---~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 166 (292)
....|-||+++.... ...-.|.. ....+|++.|+... ....|+ .|+......
T Consensus 7 ~~~~CRIC~~~~~~~--~~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Ce--iC~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYDVV--TNYCNCKNENKIVHKECLEEWINTS-----KNKSCK--ICNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCCCc--cCCcccCCCchHHHHHHHHHHHhcC-----CCCccc--ccCCeEEEE
Confidence 368999999875422 22224444 56899999999853 567898 688766543
No 243
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.13 E-value=91 Score=26.81 Aligned_cols=39 Identities=18% Similarity=0.415 Sum_probs=26.8
Q ss_pred HHHHHHHhCCeeecCCCCee---EEecCCcCeEEe-ccCcceeec
Q 048441 207 KLKKLAVEMKWKRCPNCGYY---VEKFRGCNIIIC-RCGTSFHYY 247 (292)
Q Consensus 207 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~FC~~ 247 (292)
.+.+++. .+-.||.|+.+ +.|.++=..+.| .||..-.-.
T Consensus 90 ~l~~yi~--~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 90 AIDAYVD--EYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred HHHHHHH--heEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccc
Confidence 3444454 57899999976 666666667888 588765443
No 244
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=26.90 E-value=47 Score=24.78 Aligned_cols=29 Identities=34% Similarity=0.678 Sum_probs=22.1
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
..-.||.|+..-.+..+----.| .|+..|
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 34689999999888776667788 687766
No 245
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=26.45 E-value=33 Score=24.05 Aligned_cols=38 Identities=16% Similarity=0.544 Sum_probs=27.4
Q ss_pred CcccccccccCCCCCceeecCC--CCccch-hhHHHHHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGC--SHSYCT-DCIIKYVASK 144 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~C--gH~fC~-~Cl~~~i~~~ 144 (292)
...|.+|+.+++.+..++..+= -+.||- +|...|....
T Consensus 11 ~~sC~vC~KEIPl~~a~t~E~~eYV~hFCGLeCY~~w~a~~ 51 (70)
T PF11809_consen 11 TTSCCVCCKEIPLDAAFTPEAAEYVEHFCGLECYQRWQARA 51 (70)
T ss_pred cchHHHHhhhCChhhccCcchHHHHHHHhhHHHHHHHHHHH
Confidence 6899999999987766543211 255775 9999998654
No 246
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.44 E-value=38 Score=38.39 Aligned_cols=27 Identities=33% Similarity=0.625 Sum_probs=22.8
Q ss_pred eecCCCCee------EEecCCcCeEEe-ccCcceee
Q 048441 218 KRCPNCGYY------VEKFRGCNIIIC-RCGTSFHY 246 (292)
Q Consensus 218 k~CP~C~~~------iek~~GCnhm~C-~C~~~FC~ 246 (292)
..||-|+.. +...+||. +| .||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 349999999 88889997 99 79988774
No 247
>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=26.38 E-value=64 Score=25.05 Aligned_cols=35 Identities=14% Similarity=0.279 Sum_probs=26.1
Q ss_pred CeeecCCCCeeEEecCCcCeEEe-ccCcceeeccccC
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIIC-RCGTSFHYYSRAD 251 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~ 251 (292)
+.+.|..|+...-...+.. ..| .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 5578999998876555544 888 7999999999876
No 248
>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 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=26.15 E-value=47 Score=22.57 Aligned_cols=16 Identities=38% Similarity=0.536 Sum_probs=8.8
Q ss_pred eeecCCCCeeEEecCC
Q 048441 217 WKRCPNCGYYVEKFRG 232 (292)
Q Consensus 217 ~k~CP~C~~~iek~~G 232 (292)
..+||.|+..++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 4689999999986443
No 250
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=25.75 E-value=51 Score=25.34 Aligned_cols=26 Identities=27% Similarity=0.706 Sum_probs=15.9
Q ss_pred eecCCCCeeEEecCCcCeEEe-ccCcce
Q 048441 218 KRCPNCGYYVEKFRGCNIIIC-RCGTSF 244 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C-~C~~~F 244 (292)
..||+|..-.--.+|= .|.| -|.++|
T Consensus 4 p~cp~c~sEytYed~~-~~~cpec~~ew 30 (112)
T COG2824 4 PPCPKCNSEYTYEDGG-QLICPECAHEW 30 (112)
T ss_pred CCCCccCCceEEecCc-eEeCchhcccc
Confidence 4699996655444432 7777 455554
No 251
>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=25.64 E-value=44 Score=16.95 Aligned_cols=16 Identities=31% Similarity=0.702 Sum_probs=12.9
Q ss_pred eccCCCCCccCCCCch
Q 048441 178 FCAKCKVPWHTDMKCE 193 (292)
Q Consensus 178 ~C~~C~~~~H~~~~C~ 193 (292)
.|+.|+..-|....|.
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 5899999988877765
No 252
>PLN02436 cellulose synthase A
Probab=25.53 E-value=1e+02 Score=33.28 Aligned_cols=51 Identities=24% Similarity=0.603 Sum_probs=34.8
Q ss_pred CCcccccccccCCC---CC-ceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSP---NE-SFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~---~~-~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
....|+||-|++-. .+ ++.+-.|+-..|+.|+ .|-.. + ..-.|| .|+....
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~---e--g~~~Cp--qckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERR---E--GNQACP--QCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---c--CCccCc--ccCCchh
Confidence 46799999998732 22 4445678889999999 55443 2 446898 5776543
No 253
>COG4640 Predicted membrane protein [Function unknown]
Probab=25.00 E-value=31 Score=32.78 Aligned_cols=8 Identities=63% Similarity=1.501 Sum_probs=5.9
Q ss_pred eecCCCCe
Q 048441 218 KRCPNCGY 225 (292)
Q Consensus 218 k~CP~C~~ 225 (292)
+.||+||.
T Consensus 2 ~fC~kcG~ 9 (465)
T COG4640 2 KFCPKCGS 9 (465)
T ss_pred Cccccccc
Confidence 46888884
No 254
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=24.55 E-value=88 Score=22.83 Aligned_cols=24 Identities=25% Similarity=0.793 Sum_probs=19.8
Q ss_pred cCCCCccchhhHHHHHHHHHhcCccccCCCC
Q 048441 126 KGCSHSYCTDCIIKYVASKLQESITTIGCPV 156 (292)
Q Consensus 126 ~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 156 (292)
-.|.|.|-.-|+.+|+.+ +=.||.
T Consensus 52 G~CnHaFH~HCI~rWL~T-------k~~CPl 75 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDT-------KGVCPL 75 (88)
T ss_pred EecchHHHHHHHHHHHhh-------CCCCCC
Confidence 359999999999999985 456774
No 255
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.26 E-value=55 Score=29.65 Aligned_cols=24 Identities=33% Similarity=0.780 Sum_probs=17.5
Q ss_pred eeecCCCCeeEEec--CCcCeEEe-cc
Q 048441 217 WKRCPNCGYYVEKF--RGCNIIIC-RC 240 (292)
Q Consensus 217 ~k~CP~C~~~iek~--~GCnhm~C-~C 240 (292)
-++|+.|+.+|+|. +|=+-..| .|
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 37999999999987 45555555 44
No 256
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.85 E-value=55 Score=18.68 Aligned_cols=29 Identities=21% Similarity=0.593 Sum_probs=9.2
Q ss_pred cccccccccCCCCCceeecCCCCccchhh
Q 048441 108 FVCEICVESKSPNESFRIKGCSHSYCTDC 136 (292)
Q Consensus 108 ~~C~IC~~~~~~~~~~~~~~CgH~fC~~C 136 (292)
+.|.+|-.+...........|.-.+...|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp ---TTTS----S--EEE-TTT-----HHH
T ss_pred CcCCcCCCcCCCCceEECccCCCccChhc
Confidence 46788887665534455566776666655
No 257
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=23.73 E-value=67 Score=19.70 Aligned_cols=35 Identities=17% Similarity=0.537 Sum_probs=21.1
Q ss_pred CCcccccccccCCCCC---ceeecCCCCccch-hhHHHH
Q 048441 106 PSFVCEICVESKSPNE---SFRIKGCSHSYCT-DCIIKY 140 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~---~~~~~~CgH~fC~-~Cl~~~ 140 (292)
....|.-|-..+.... .+...+-.|.||. .|+..|
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHHhhC
Confidence 3688999998886555 2444467788987 677654
No 258
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=23.10 E-value=29 Score=23.74 Aligned_cols=35 Identities=17% Similarity=0.280 Sum_probs=26.8
Q ss_pred eecCCCCeeEEec--CCcCeEEe-ccCcceeeccccCc
Q 048441 218 KRCPNCGYYVEKF--RGCNIIIC-RCGTSFHYYSRADL 252 (292)
Q Consensus 218 k~CP~C~~~iek~--~GCnhm~C-~C~~~FC~~C~~~~ 252 (292)
..||-|++..-.. +-=|+=+| .|+...|-.||-.-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 4699999877221 34689999 89999999999554
No 259
>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=23.03 E-value=30 Score=31.90 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=21.0
Q ss_pred eecCCCCeeEEecCCcCeEEeccCcceeeccccC
Q 048441 218 KRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRAD 251 (292)
Q Consensus 218 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~ 251 (292)
..||.|+...-.+..=.-|+=.|||.||-.|...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDL 37 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHH
Confidence 4699999965444221112115888888888776
No 260
>PRK12495 hypothetical protein; Provisional
Probab=22.94 E-value=71 Score=27.90 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=22.5
Q ss_pred CeeecCCCCeeEEecCCcCeEEeccCcceeeccccCccC
Q 048441 216 KWKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSE 254 (292)
Q Consensus 216 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 254 (292)
..+.||.|+.+|.+..|+ .||-.|......
T Consensus 41 sa~hC~~CG~PIpa~pG~---------~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ---------EFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccCCCCe---------eECCCCCCcccc
Confidence 447899999999977674 567777766553
No 261
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.87 E-value=40 Score=35.53 Aligned_cols=24 Identities=46% Similarity=1.131 Sum_probs=18.2
Q ss_pred eecCCCCee-EEecCCcCeEEe-ccCcc
Q 048441 218 KRCPNCGYY-VEKFRGCNIIIC-RCGTS 243 (292)
Q Consensus 218 k~CP~C~~~-iek~~GCnhm~C-~C~~~ 243 (292)
-.||-|+.- |+..+||| +| .||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 489999875 78889998 46 56544
No 262
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.82 E-value=19 Score=34.45 Aligned_cols=33 Identities=15% Similarity=0.336 Sum_probs=22.3
Q ss_pred eeecCCCCeeEEecCCcCeEEeccCcceeeccccCccC
Q 048441 217 WKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADLSE 254 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 254 (292)
.-.||-|.-.+. +.++=.|||.||+.|...|-.
T Consensus 26 ~l~C~IC~d~~~-----~PvitpCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 26 SLRCHICKDFFD-----VPVLTSCSHTFCSLCIRRCLS 58 (397)
T ss_pred ccCCCcCchhhh-----CccCCCCCCchhHHHHHHHHh
Confidence 468999987763 222225888888888876543
No 263
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.51 E-value=70 Score=24.96 Aligned_cols=9 Identities=44% Similarity=1.043 Sum_probs=5.2
Q ss_pred cCCCCeeEE
Q 048441 220 CPNCGYYVE 228 (292)
Q Consensus 220 CP~C~~~ie 228 (292)
||.|+..+.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 666665543
No 264
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=22.43 E-value=1.5e+02 Score=22.64 Aligned_cols=31 Identities=23% Similarity=0.691 Sum_probs=22.9
Q ss_pred CCccchhhHHHHHHHHHhc--CccccCCCCCCCCC
Q 048441 129 SHSYCTDCIIKYVASKLQE--SITTIGCPVTGCQG 161 (292)
Q Consensus 129 gH~fC~~Cl~~~i~~~i~~--~~~~i~CP~~~C~~ 161 (292)
.-.||..||.......+.+ ......|| .|.+
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECC--CCCC
Confidence 6789999999988876644 22457888 5664
No 265
>PLN02189 cellulose synthase
Probab=22.34 E-value=1.2e+02 Score=32.57 Aligned_cols=51 Identities=27% Similarity=0.610 Sum_probs=35.0
Q ss_pred CCcccccccccCCC----CCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCCCCC
Q 048441 106 PSFVCEICVESKSP----NESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQGVLE 164 (292)
Q Consensus 106 ~~~~C~IC~~~~~~----~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 164 (292)
....|.||.|++.. ...+.+-.|+-..|+.|. +|-.. + ..-.|| .|+....
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~---e--g~q~Cp--qCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERR---E--GTQNCP--QCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---c--CCccCc--ccCCchh
Confidence 46799999998642 234455678899999999 55443 2 446898 5776543
No 266
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.21 E-value=52 Score=34.38 Aligned_cols=41 Identities=24% Similarity=0.497 Sum_probs=31.6
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
.-.|..|--++..+.+.. .|||.|...|+. + ..-.|| .|..
T Consensus 840 ~skCs~C~~~LdlP~VhF--~CgHsyHqhC~e--------~--~~~~CP--~C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVHF--LCGHSYHQHCLE--------D--KEDKCP--KCLP 880 (933)
T ss_pred eeeecccCCccccceeee--ecccHHHHHhhc--------c--CcccCC--ccch
Confidence 468999998887665544 599999999998 2 446898 6775
No 267
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.10 E-value=74 Score=29.39 Aligned_cols=38 Identities=18% Similarity=0.442 Sum_probs=24.9
Q ss_pred cccCCCCCCCCCCCCHHHHHh--hCCCCceeccCCCCCccCC
Q 048441 150 TTIGCPVTGCQGVLEPEYCRN--ILPQQVMFCAKCKVPWHTD 189 (292)
Q Consensus 150 ~~i~CP~~~C~~~l~~~~i~~--~l~~~~~~C~~C~~~~H~~ 189 (292)
..-.|| .|++.-....++. --......|..|...||..
T Consensus 186 ~~~~CP--vCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~ 225 (309)
T PRK03564 186 QRQFCP--VCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV 225 (309)
T ss_pred CCCCCC--CCCCcchhheeeccCCCCceEEEcCCCCCccccc
Confidence 467999 6887655443321 1112238999999999975
No 268
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.08 E-value=72 Score=24.87 Aligned_cols=10 Identities=20% Similarity=0.630 Sum_probs=7.3
Q ss_pred eeecCCCCee
Q 048441 217 WKRCPNCGYY 226 (292)
Q Consensus 217 ~k~CP~C~~~ 226 (292)
+.+||+|+..
T Consensus 88 ~~~CP~Cgs~ 97 (117)
T PRK00564 88 YGVCEKCHSK 97 (117)
T ss_pred CCcCcCCCCC
Confidence 3469999875
No 269
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=21.98 E-value=19 Score=25.96 Aligned_cols=49 Identities=22% Similarity=0.571 Sum_probs=32.6
Q ss_pred CcccccccccCC---------CCCceee-cCCCCccchhhHHHHHHHHHhcCccccCCCCCCCCC
Q 048441 107 SFVCEICVESKS---------PNESFRI-KGCSHSYCTDCIIKYVASKLQESITTIGCPVTGCQG 161 (292)
Q Consensus 107 ~~~C~IC~~~~~---------~~~~~~~-~~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 161 (292)
..+|.||.-++. +++...+ -.|.|.|-.-|+.+|+.+.-.+ -.|| -|+.
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq----~~CP--mcRq 78 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ----GQCP--MCRQ 78 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc----ccCC--cchh
Confidence 458888877663 2332211 2588999999999999865433 5677 4654
No 270
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.85 E-value=38 Score=30.60 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=19.0
Q ss_pred eeecCCCCeeEEecCCcCeEEe-ccCcceeeccccC
Q 048441 217 WKRCPNCGYYVEKFRGCNIIIC-RCGTSFHYYSRAD 251 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~ 251 (292)
...||-|+..=. +-|+= +|+|.+||.|...
T Consensus 239 ~~~C~~Cg~~Pt-----iP~~~~~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPT-----IPHVIGKCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCC-----CCeeeccccceeehhhhhh
Confidence 368999998632 12222 4677777777654
No 271
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=21.42 E-value=51 Score=25.03 Aligned_cols=30 Identities=23% Similarity=0.582 Sum_probs=21.6
Q ss_pred CCcccccccccCCCCCceeecCCCCccchhh
Q 048441 106 PSFVCEICVESKSPNESFRIKGCSHSYCTDC 136 (292)
Q Consensus 106 ~~~~C~IC~~~~~~~~~~~~~~CgH~fC~~C 136 (292)
..|+|.-||=-...+++.. ..=|+.+|++|
T Consensus 69 DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 3699999996544444443 34689999998
No 272
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.06 E-value=26 Score=34.27 Aligned_cols=31 Identities=19% Similarity=0.224 Sum_probs=20.5
Q ss_pred eeecCCCCeeEEecCCcCeEEeccCcceeeccccCc
Q 048441 217 WKRCPNCGYYVEKFRGCNIIICRCGTSFHYYSRADL 252 (292)
Q Consensus 217 ~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~ 252 (292)
-..||-|-..-.- -.|| .|||.|||-|+-.+
T Consensus 186 ~~~CPICL~~~~~----p~~t-~CGHiFC~~CiLqy 216 (513)
T KOG2164|consen 186 DMQCPICLEPPSV----PVRT-NCGHIFCGPCILQY 216 (513)
T ss_pred CCcCCcccCCCCc----cccc-ccCceeeHHHHHHH
Confidence 4689999765431 1122 29999999997653
No 273
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=21.00 E-value=84 Score=20.40 Aligned_cols=32 Identities=25% Similarity=0.627 Sum_probs=24.6
Q ss_pred CcccccccccCCCCCceeecCCCCccchhhHHHH
Q 048441 107 SFVCEICVESKSPNESFRIKGCSHSYCTDCIIKY 140 (292)
Q Consensus 107 ~~~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~ 140 (292)
=|.|..|-..+.....+. .=+..||..|..+.
T Consensus 26 Cf~C~~C~~~l~~~~~~~--~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYE--KDGKPYCKDCYQKR 57 (58)
T ss_dssp TSBETTTTCBTTTSSEEE--ETTEEEEHHHHHHH
T ss_pred ccccCCCCCccCCCeeEe--ECCEEECHHHHhhh
Confidence 589999999887766443 35689999998764
No 274
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.62 E-value=58 Score=29.01 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=18.4
Q ss_pred ecCCCCeeEEecCCcCeEEeccCcce
Q 048441 219 RCPNCGYYVEKFRGCNIIICRCGTSF 244 (292)
Q Consensus 219 ~CP~C~~~iek~~GCnhm~C~C~~~F 244 (292)
.||.|+.++...+ +...|..+|.|
T Consensus 4 ~CP~C~~~l~~~~--~~~~C~~~h~f 27 (272)
T PRK11088 4 QCPLCHQPLTLEE--NSWICPQNHQF 27 (272)
T ss_pred cCCCCCcchhcCC--CEEEcCCCCCC
Confidence 6999999996644 46888667776
No 275
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.58 E-value=59 Score=30.01 Aligned_cols=33 Identities=24% Similarity=0.627 Sum_probs=25.9
Q ss_pred eecCCCCee-----EE--ecCCcCeEEe-ccCcce------eecccc
Q 048441 218 KRCPNCGYY-----VE--KFRGCNIIIC-RCGTSF------HYYSRA 250 (292)
Q Consensus 218 k~CP~C~~~-----ie--k~~GCnhm~C-~C~~~F------C~~C~~ 250 (292)
..||-|+.. |. -.+|=.++.| .|+++| |-.|+.
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 579999987 22 1368899999 799988 668886
No 276
>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=20.42 E-value=53 Score=21.22 Aligned_cols=35 Identities=26% Similarity=0.568 Sum_probs=25.6
Q ss_pred ccccccccCCCCCceeecCCCCccchhhHHHHHHHHHhc
Q 048441 109 VCEICVESKSPNESFRIKGCSHSYCTDCIIKYVASKLQE 147 (292)
Q Consensus 109 ~C~IC~~~~~~~~~~~~~~CgH~fC~~Cl~~~i~~~i~~ 147 (292)
.|.||-..... -+.+ .|..+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~~--GI~I--~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEE--GIHI--YGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCC--CEEE--ECeEehHHHHHHhccCCCCC
Confidence 48888876543 3333 78999999999998866544
No 277
>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=20.04 E-value=38 Score=19.95 Aligned_cols=9 Identities=56% Similarity=1.261 Sum_probs=6.4
Q ss_pred ecCCCCeeE
Q 048441 219 RCPNCGYYV 227 (292)
Q Consensus 219 ~CP~C~~~i 227 (292)
-||+|++.|
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999865
Done!