Query 008947
Match_columns 548
No_of_seqs 418 out of 1602
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 18:32:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008947hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 2.1E-69 4.6E-74 580.8 26.5 429 41-497 2-437 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 6E-35 1.3E-39 306.4 10.0 269 68-363 85-374 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 2.6E-34 5.7E-39 290.1 12.2 203 115-322 183-415 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 1E-24 2.2E-29 213.1 8.0 194 113-315 218-439 (446)
5 smart00647 IBR In Between Ring 99.2 1.3E-11 2.8E-16 97.0 5.8 62 190-252 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 1.4E-11 3E-16 96.7 0.4 62 190-252 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.5 5E-08 1.1E-12 70.1 2.2 41 119-165 1-41 (42)
8 PF13639 zf-RING_2: Ring finge 98.1 1.3E-06 2.8E-11 63.4 2.0 40 118-165 2-42 (44)
9 PF13923 zf-C3HC4_2: Zinc fing 98.1 1.5E-06 3.3E-11 61.3 2.2 37 119-165 1-38 (39)
10 PF00097 zf-C3HC4: Zinc finger 98.1 2.1E-06 4.6E-11 61.1 2.5 39 119-165 1-40 (41)
11 smart00647 IBR In Between Ring 98.1 4.8E-06 1E-10 65.1 4.5 38 275-312 17-59 (64)
12 PF01485 IBR: IBR domain; Int 98.0 2.8E-06 6E-11 66.4 1.9 38 275-312 17-59 (64)
13 KOG0320 Predicted E3 ubiquitin 97.9 4.6E-06 9.9E-11 77.1 2.3 54 113-176 128-181 (187)
14 PLN03208 E3 ubiquitin-protein 97.9 6.8E-06 1.5E-10 77.9 3.4 65 114-182 16-88 (193)
15 PF13445 zf-RING_UBOX: RING-ty 97.9 5.8E-06 1.2E-10 59.5 2.1 41 119-164 1-43 (43)
16 cd00162 RING RING-finger (Real 97.7 2.4E-05 5.2E-10 55.9 2.9 44 118-171 1-44 (45)
17 PF14634 zf-RING_5: zinc-RING 97.7 1.8E-05 3.8E-10 57.4 2.2 42 118-169 1-43 (44)
18 PF13920 zf-C3HC4_3: Zinc fing 97.7 2.6E-05 5.6E-10 58.1 2.8 46 116-173 2-48 (50)
19 KOG0823 Predicted E3 ubiquitin 97.5 3.6E-05 7.8E-10 74.3 1.8 60 113-181 44-103 (230)
20 smart00184 RING Ring finger. E 97.4 8.7E-05 1.9E-09 51.0 2.4 30 119-150 1-30 (39)
21 smart00504 Ubox Modified RING 97.4 0.00013 2.8E-09 56.8 3.1 47 117-175 2-48 (63)
22 KOG2164 Predicted E3 ubiquitin 97.4 5.9E-05 1.3E-09 80.3 0.9 60 116-182 186-245 (513)
23 PHA02926 zinc finger-like prot 97.3 0.00012 2.6E-09 70.3 2.5 56 113-172 167-229 (242)
24 KOG0317 Predicted E3 ubiquitin 97.3 0.0001 2.2E-09 73.3 1.7 50 115-176 238-287 (293)
25 KOG2177 Predicted E3 ubiquitin 97.3 0.00013 2.9E-09 73.8 2.5 44 115-170 12-55 (386)
26 PHA02929 N1R/p28-like protein; 97.2 0.00019 4.1E-09 70.9 3.0 50 114-173 172-227 (238)
27 TIGR00599 rad18 DNA repair pro 97.2 0.00024 5.2E-09 75.2 3.2 50 114-175 24-73 (397)
28 KOG4367 Predicted Zn-finger pr 97.1 0.0032 7E-08 65.6 10.3 35 115-151 3-37 (699)
29 KOG0287 Postreplication repair 96.9 0.00066 1.4E-08 68.6 3.1 63 115-193 22-86 (442)
30 PF11789 zf-Nse: Zinc-finger o 96.7 0.0011 2.5E-08 50.7 2.5 47 115-169 10-57 (57)
31 TIGR00570 cdk7 CDK-activating 96.7 0.00084 1.8E-08 68.4 2.2 53 117-178 4-59 (309)
32 KOG0978 E3 ubiquitin ligase in 96.3 0.00088 1.9E-08 74.9 -0.2 55 115-180 642-696 (698)
33 PF14555 UBA_4: UBA-like domai 96.2 0.014 3E-07 42.0 5.5 40 52-91 1-40 (43)
34 PF14835 zf-RING_6: zf-RING of 96.1 0.0015 3.3E-08 50.6 -0.0 43 116-172 7-50 (65)
35 KOG0804 Cytoplasmic Zn-finger 96.0 0.34 7.4E-06 51.4 16.9 115 42-170 86-219 (493)
36 PF04564 U-box: U-box domain; 95.9 0.0048 1E-07 49.8 2.0 50 115-175 3-52 (73)
37 KOG1002 Nucleotide excision re 95.7 0.0042 9.2E-08 66.2 1.3 55 114-175 534-588 (791)
38 COG5540 RING-finger-containing 95.6 0.0073 1.6E-07 60.5 2.5 52 114-174 321-373 (374)
39 COG5574 PEX10 RING-finger-cont 95.4 0.011 2.4E-07 58.3 2.9 53 115-177 214-266 (271)
40 PF12678 zf-rbx1: RING-H2 zinc 95.3 0.01 2.2E-07 47.9 2.1 41 117-165 20-71 (73)
41 KOG4628 Predicted E3 ubiquitin 95.2 0.011 2.4E-07 61.3 2.2 45 117-170 230-275 (348)
42 PF11793 FANCL_C: FANCL C-term 94.5 0.023 5.1E-07 45.5 2.0 57 116-174 2-67 (70)
43 COG5432 RAD18 RING-finger-cont 94.4 0.023 5.1E-07 56.5 2.2 47 115-173 24-70 (391)
44 KOG0006 E3 ubiquitin-protein l 94.1 0.11 2.4E-06 52.5 6.3 145 71-250 285-439 (446)
45 KOG1814 Predicted E3 ubiquitin 94.1 0.27 5.9E-06 51.6 9.3 38 274-311 271-311 (445)
46 KOG2879 Predicted E3 ubiquitin 93.8 0.052 1.1E-06 53.9 3.3 50 114-173 237-287 (298)
47 KOG1812 Predicted E3 ubiquitin 93.7 0.033 7.2E-07 59.3 1.8 41 205-249 304-344 (384)
48 PF14570 zf-RING_4: RING/Ubox 93.5 0.05 1.1E-06 40.0 2.0 44 119-171 1-46 (48)
49 PF10571 UPF0547: Uncharacteri 93.2 0.042 9.1E-07 35.1 1.0 23 277-303 1-24 (26)
50 KOG0824 Predicted E3 ubiquitin 92.9 0.05 1.1E-06 54.7 1.7 53 114-177 5-57 (324)
51 COG5243 HRD1 HRD ubiquitin lig 92.8 0.069 1.5E-06 55.1 2.4 95 65-172 236-344 (491)
52 KOG4185 Predicted E3 ubiquitin 92.3 0.19 4E-06 51.7 4.9 55 117-180 4-64 (296)
53 KOG4159 Predicted E3 ubiquitin 92.2 0.17 3.7E-06 53.9 4.6 49 114-174 82-130 (398)
54 PRK00420 hypothetical protein; 91.6 1.3 2.8E-05 38.8 8.5 27 276-310 23-49 (112)
55 KOG1428 Inhibitor of type V ad 91.3 0.33 7.1E-06 57.8 5.7 66 115-182 3485-3553(3738)
56 COG5152 Uncharacterized conser 91.1 0.068 1.5E-06 50.5 0.3 32 115-148 195-226 (259)
57 KOG2817 Predicted E3 ubiquitin 91.1 0.88 1.9E-05 47.8 8.3 126 40-177 255-389 (394)
58 TIGR00570 cdk7 CDK-activating 90.8 7.4 0.00016 40.1 14.5 53 209-290 5-57 (309)
59 KOG1039 Predicted E3 ubiquitin 90.7 0.16 3.4E-06 53.1 2.5 55 113-170 158-218 (344)
60 KOG0311 Predicted E3 ubiquitin 90.5 0.048 1E-06 56.0 -1.4 47 115-171 42-88 (381)
61 KOG0826 Predicted E3 ubiquitin 90.4 0.73 1.6E-05 47.1 6.8 79 83-172 260-347 (357)
62 KOG2660 Locus-specific chromos 89.4 0.21 4.5E-06 51.1 2.0 47 115-172 14-60 (331)
63 KOG4692 Predicted E3 ubiquitin 89.3 0.21 4.6E-06 51.2 2.0 52 111-174 417-468 (489)
64 KOG1645 RING-finger-containing 88.7 0.28 6.1E-06 51.4 2.5 49 116-172 4-55 (463)
65 KOG0802 E3 ubiquitin ligase [P 88.5 0.22 4.9E-06 55.6 1.7 45 116-170 291-338 (543)
66 COG5220 TFB3 Cdk activating ki 88.4 0.11 2.5E-06 50.4 -0.5 49 117-172 11-63 (314)
67 PF12861 zf-Apc11: Anaphase-pr 87.4 0.46 1E-05 39.3 2.5 31 135-172 51-81 (85)
68 PF13240 zinc_ribbon_2: zinc-r 87.3 0.28 6.2E-06 30.3 0.9 12 278-289 1-12 (23)
69 smart00744 RINGv The RING-vari 86.1 0.57 1.2E-05 34.7 2.1 42 118-165 1-47 (49)
70 KOG1734 Predicted RING-contain 86.0 0.38 8.3E-06 47.8 1.5 53 115-175 223-283 (328)
71 PF05883 Baculo_RING: Baculovi 84.7 0.38 8.3E-06 43.2 0.8 34 116-149 26-66 (134)
72 KOG1785 Tyrosine kinase negati 84.4 0.45 9.7E-06 49.7 1.2 45 117-169 370-414 (563)
73 KOG1815 Predicted E3 ubiquitin 84.1 0.62 1.3E-05 50.8 2.2 37 276-312 158-197 (444)
74 PHA00626 hypothetical protein 84.0 0.75 1.6E-05 34.7 1.9 29 278-306 2-36 (59)
75 smart00661 RPOL9 RNA polymeras 83.9 0.81 1.7E-05 33.9 2.1 27 277-303 1-30 (52)
76 KOG4265 Predicted E3 ubiquitin 83.9 0.95 2.1E-05 47.0 3.3 48 114-173 288-336 (349)
77 PRK14559 putative protein seri 83.7 0.69 1.5E-05 52.6 2.4 25 277-312 28-52 (645)
78 KOG0828 Predicted E3 ubiquitin 83.3 0.5 1.1E-05 50.6 1.1 51 114-173 569-634 (636)
79 PF00627 UBA: UBA/TS-N domain; 83.2 4.1 8.9E-05 28.0 5.3 34 52-86 3-36 (37)
80 KOG4739 Uncharacterized protei 83.0 0.37 8E-06 47.4 -0.0 47 117-175 4-50 (233)
81 COG4647 AcxC Acetone carboxyla 82.1 3.3 7.2E-05 36.7 5.5 109 172-287 17-131 (165)
82 KOG0825 PHD Zn-finger protein 82.0 0.84 1.8E-05 51.5 2.2 17 136-152 121-137 (1134)
83 KOG1001 Helicase-like transcri 81.7 0.61 1.3E-05 53.3 1.0 47 117-174 455-501 (674)
84 PF14952 zf-tcix: Putative tre 81.4 1 2.2E-05 32.3 1.7 30 270-303 5-37 (44)
85 PF13248 zf-ribbon_3: zinc-rib 81.3 0.82 1.8E-05 29.1 1.1 13 277-289 3-15 (26)
86 KOG0823 Predicted E3 ubiquitin 80.5 0.81 1.8E-05 44.7 1.3 47 215-287 49-95 (230)
87 PLN03086 PRLI-interacting fact 80.3 3.7 8E-05 45.8 6.4 57 159-238 406-463 (567)
88 TIGR00622 ssl1 transcription f 79.4 0.86 1.9E-05 39.8 1.0 38 208-248 56-101 (112)
89 KOG0317 Predicted E3 ubiquitin 78.4 0.39 8.5E-06 48.3 -1.6 35 272-312 235-270 (293)
90 KOG4172 Predicted E3 ubiquitin 77.9 0.7 1.5E-05 34.7 0.0 45 117-172 8-53 (62)
91 PRK00432 30S ribosomal protein 77.9 1.2 2.6E-05 33.2 1.2 28 274-303 18-47 (50)
92 KOG0827 Predicted E3 ubiquitin 77.4 0.86 1.9E-05 47.6 0.4 47 117-170 5-53 (465)
93 PF02845 CUE: CUE domain; Int 76.7 9.5 0.00021 27.0 5.6 38 52-89 2-40 (42)
94 KOG4445 Uncharacterized conser 76.4 6.8 0.00015 39.8 6.4 37 117-153 116-153 (368)
95 KOG3800 Predicted E3 ubiquitin 76.0 2.9 6.4E-05 42.2 3.7 48 118-174 2-52 (300)
96 PF09297 zf-NADH-PPase: NADH p 75.7 3.2 7E-05 27.6 2.8 28 275-302 2-30 (32)
97 KOG0297 TNF receptor-associate 75.0 1.4 2.9E-05 47.3 1.2 37 113-151 18-55 (391)
98 KOG1813 Predicted E3 ubiquitin 74.8 0.99 2.2E-05 45.6 0.1 44 116-171 241-284 (313)
99 PF14835 zf-RING_6: zf-RING of 73.7 2.2 4.8E-05 33.4 1.8 34 277-310 8-49 (65)
100 PF13719 zinc_ribbon_5: zinc-r 73.0 3.1 6.8E-05 28.8 2.2 28 208-238 3-35 (37)
101 PF13717 zinc_ribbon_4: zinc-r 72.1 3.4 7.4E-05 28.5 2.2 28 208-238 3-35 (36)
102 KOG2807 RNA polymerase II tran 72.1 1.3 2.9E-05 45.2 0.3 84 138-248 276-365 (378)
103 PF04641 Rtf2: Rtf2 RING-finge 71.5 3.1 6.6E-05 42.1 2.7 58 114-182 111-170 (260)
104 PF10367 Vps39_2: Vacuolar sor 71.1 1.6 3.4E-05 37.3 0.5 31 116-146 78-108 (109)
105 PRK00398 rpoP DNA-directed RNA 70.1 3.6 7.8E-05 29.8 2.1 28 277-304 4-32 (46)
106 cd00194 UBA Ubiquitin Associat 69.9 15 0.00033 25.0 5.2 34 54-88 4-37 (38)
107 PRK14559 putative protein seri 69.6 3.2 7E-05 47.3 2.6 12 276-287 41-52 (645)
108 PF15227 zf-C3HC4_4: zinc fing 69.4 2 4.3E-05 30.7 0.6 28 279-311 1-28 (42)
109 PF00643 zf-B_box: B-box zinc 69.3 3.2 6.8E-05 29.2 1.6 32 277-315 4-37 (42)
110 KOG3039 Uncharacterized conser 69.1 2.7 5.9E-05 41.4 1.6 53 115-177 220-274 (303)
111 COG5175 MOT2 Transcriptional r 68.5 1.9 4.1E-05 44.2 0.5 53 116-177 14-68 (480)
112 smart00165 UBA Ubiquitin assoc 67.9 14 0.00031 25.0 4.7 33 54-87 4-36 (37)
113 PRK04023 DNA polymerase II lar 66.1 4.3 9.4E-05 47.7 2.7 36 201-246 620-661 (1121)
114 PF02150 RNA_POL_M_15KD: RNA p 66.0 3.4 7.4E-05 28.3 1.2 27 208-237 2-29 (35)
115 PHA03096 p28-like protein; Pro 66.0 3.4 7.3E-05 42.3 1.7 37 117-153 179-221 (284)
116 KOG0320 Predicted E3 ubiquitin 65.5 1.7 3.8E-05 40.8 -0.4 29 233-287 150-178 (187)
117 COG5222 Uncharacterized conser 65.4 3.2 7E-05 41.9 1.4 43 117-170 275-318 (427)
118 KOG1701 Focal adhesion adaptor 65.0 3.8 8.2E-05 43.6 1.8 10 118-127 276-285 (468)
119 PF05320 Pox_RNA_Pol_19: Poxvi 64.9 2.8 6.2E-05 38.3 0.8 10 115-124 125-134 (167)
120 PF08274 PhnA_Zn_Ribbon: PhnA 64.3 5 0.00011 26.6 1.7 26 277-303 3-29 (30)
121 smart00546 CUE Domain that may 63.9 26 0.00057 24.7 5.6 38 52-89 3-41 (43)
122 KOG3002 Zn finger protein [Gen 63.6 10 0.00022 39.1 4.7 53 113-181 45-97 (299)
123 KOG1952 Transcription factor N 63.3 4.5 9.8E-05 46.5 2.2 50 115-165 190-241 (950)
124 TIGR02098 MJ0042_CXXC MJ0042 f 63.3 7.1 0.00015 26.9 2.4 28 208-238 3-35 (38)
125 KOG2906 RNA polymerase III sub 62.5 4.9 0.00011 34.0 1.7 28 277-304 2-32 (105)
126 cd00021 BBOX B-Box-type zinc f 62.3 6.8 0.00015 26.7 2.2 31 278-315 2-34 (39)
127 PRK08665 ribonucleotide-diphos 62.3 4.2 9.1E-05 47.3 1.8 26 277-304 725-751 (752)
128 COG1998 RPS31 Ribosomal protei 61.9 5.5 0.00012 29.4 1.7 26 276-301 19-45 (51)
129 PRK14714 DNA polymerase II lar 61.6 6.3 0.00014 47.5 3.0 29 472-500 846-881 (1337)
130 PF07191 zinc-ribbons_6: zinc- 59.8 6.6 0.00014 31.3 2.0 32 278-311 3-40 (70)
131 PLN03208 E3 ubiquitin-protein 59.7 3.5 7.5E-05 39.6 0.4 32 276-312 18-49 (193)
132 PF07282 OrfB_Zn_ribbon: Putat 59.5 6.8 0.00015 30.8 2.0 28 275-302 27-55 (69)
133 KOG0978 E3 ubiquitin ligase in 59.1 3.4 7.4E-05 47.0 0.3 30 233-287 660-689 (698)
134 KOG3970 Predicted E3 ubiquitin 59.0 6.5 0.00014 38.3 2.1 54 117-172 51-104 (299)
135 PF14447 Prok-RING_4: Prokaryo 58.1 4.2 9.2E-05 30.8 0.6 45 116-174 7-51 (55)
136 KOG2177 Predicted E3 ubiquitin 58.1 5.7 0.00012 39.7 1.7 24 278-308 88-112 (386)
137 PF07975 C1_4: TFIIH C1-like d 57.5 4 8.7E-05 30.5 0.4 35 215-249 4-42 (51)
138 PF14369 zf-RING_3: zinc-finge 57.1 8.5 0.00018 26.4 1.9 28 208-238 3-31 (35)
139 PF09538 FYDLN_acid: Protein o 56.7 6.2 0.00014 34.4 1.5 25 277-303 10-36 (108)
140 KOG1941 Acetylcholine receptor 56.2 4.2 9.2E-05 42.6 0.4 48 115-170 364-413 (518)
141 COG1198 PriA Primosomal protei 55.5 8.7 0.00019 44.4 2.8 35 276-310 444-484 (730)
142 PRK05654 acetyl-CoA carboxylas 55.5 3 6.4E-05 42.9 -0.8 28 276-303 27-56 (292)
143 PF06677 Auto_anti-p27: Sjogre 55.2 10 0.00022 27.0 2.1 22 277-300 18-41 (41)
144 PF10168 Nup88: Nuclear pore c 54.5 3.1E+02 0.0067 32.0 15.1 48 432-480 601-648 (717)
145 KOG3579 Predicted E3 ubiquitin 54.4 14 0.00031 37.3 3.7 54 114-170 266-322 (352)
146 PF14569 zf-UDP: Zinc-binding 54.2 6.2 0.00013 32.0 0.9 54 215-293 14-68 (80)
147 PF08938 HBS1_N: HBS1 N-termin 53.7 1.2 2.7E-05 36.4 -3.2 48 42-90 20-70 (79)
148 KOG1493 Anaphase-promoting com 53.4 3.5 7.5E-05 33.3 -0.6 48 118-172 22-80 (84)
149 PRK14714 DNA polymerase II lar 52.9 8.5 0.00018 46.4 2.2 55 441-496 800-858 (1337)
150 COG1645 Uncharacterized Zn-fin 52.8 8.4 0.00018 34.6 1.7 24 276-308 28-51 (131)
151 KOG2932 E3 ubiquitin ligase in 52.7 5.4 0.00012 40.7 0.5 54 203-292 86-139 (389)
152 smart00661 RPOL9 RNA polymeras 52.4 11 0.00024 27.7 2.1 26 209-237 2-29 (52)
153 PRK00398 rpoP DNA-directed RNA 52.0 15 0.00032 26.6 2.6 28 209-240 5-33 (46)
154 TIGR03655 anti_R_Lar restricti 50.4 13 0.00029 27.8 2.2 11 277-287 2-12 (53)
155 KOG3130 Uncharacterized conser 50.3 13 0.00029 39.2 2.9 6 121-126 396-401 (514)
156 TIGR00595 priA primosomal prot 50.2 13 0.00028 41.3 3.0 34 277-310 223-262 (505)
157 PF07191 zinc-ribbons_6: zinc- 49.7 4 8.6E-05 32.6 -0.8 39 117-172 2-40 (70)
158 PF13834 DUF4193: Domain of un 49.4 6.9 0.00015 33.3 0.6 33 112-144 66-98 (99)
159 PF12773 DZR: Double zinc ribb 48.9 7.7 0.00017 28.4 0.7 12 277-288 30-41 (50)
160 COG5219 Uncharacterized conser 48.6 8.8 0.00019 44.7 1.4 51 115-173 1468-1523(1525)
161 CHL00174 accD acetyl-CoA carbo 48.5 4.3 9.3E-05 41.7 -1.0 27 277-303 39-67 (296)
162 TIGR01384 TFS_arch transcripti 48.4 12 0.00025 32.1 1.8 24 277-302 1-25 (104)
163 PF02318 FYVE_2: FYVE-type zin 48.1 28 0.0006 30.7 4.2 42 275-317 53-95 (118)
164 KOG2034 Vacuolar sorting prote 47.7 9.7 0.00021 44.2 1.5 39 115-153 816-854 (911)
165 PF14803 Nudix_N_2: Nudix N-te 47.2 14 0.00031 25.1 1.7 27 208-237 1-31 (34)
166 TIGR00515 accD acetyl-CoA carb 46.2 5.1 0.00011 41.0 -0.8 28 276-303 26-55 (285)
167 PF14445 Prok-RING_2: Prokaryo 46.2 4.6 0.0001 29.9 -0.8 34 115-148 6-40 (57)
168 KOG3268 Predicted E3 ubiquitin 46.0 18 0.00038 34.1 2.7 57 115-173 164-228 (234)
169 smart00336 BBOX B-Box-type zin 45.8 19 0.00041 24.8 2.3 32 277-315 4-37 (42)
170 cd07666 BAR_SNX7 The Bin/Amphi 45.6 2.9E+02 0.0063 27.7 11.4 99 383-492 140-238 (243)
171 PRK14873 primosome assembly pr 45.5 15 0.00033 42.2 2.7 34 277-310 393-431 (665)
172 KOG4275 Predicted E3 ubiquitin 45.3 9.2 0.0002 38.8 0.8 28 116-145 300-328 (350)
173 COG1997 RPL43A Ribosomal prote 45.3 16 0.00035 30.3 2.1 28 276-303 35-63 (89)
174 PF10446 DUF2457: Protein of u 45.2 15 0.00032 39.5 2.4 19 109-127 187-205 (458)
175 COG5151 SSL1 RNA polymerase II 44.2 6.6 0.00014 40.0 -0.4 89 137-248 307-408 (421)
176 COG5574 PEX10 RING-finger-cont 43.8 7.1 0.00015 39.1 -0.2 37 114-150 93-132 (271)
177 KOG1940 Zn-finger protein [Gen 43.8 19 0.00041 36.7 2.7 46 115-170 157-204 (276)
178 PF12906 RINGv: RING-variant d 43.5 20 0.00043 26.2 2.2 33 119-151 1-38 (47)
179 COG0777 AccD Acetyl-CoA carbox 42.8 8.3 0.00018 38.9 0.1 28 276-303 28-57 (294)
180 KOG3161 Predicted E3 ubiquitin 42.6 9.5 0.00021 42.6 0.5 36 116-151 11-48 (861)
181 PF01599 Ribosomal_S27: Riboso 42.6 18 0.00038 26.6 1.7 26 276-301 18-46 (47)
182 PF03943 TAP_C: TAP C-terminal 42.4 31 0.00067 25.7 3.1 37 53-89 2-38 (51)
183 smart00804 TAP_C C-terminal do 41.3 1.1E+02 0.0023 24.0 6.1 41 49-89 10-50 (63)
184 PF03119 DNA_ligase_ZBD: NAD-d 41.2 25 0.00054 22.8 2.1 20 278-297 1-20 (28)
185 PRK05580 primosome assembly pr 40.8 21 0.00046 41.2 3.0 34 277-310 391-430 (679)
186 PF12959 DUF3848: Protein of u 40.8 1.1E+02 0.0025 26.2 6.5 49 41-90 23-76 (101)
187 PF01363 FYVE: FYVE zinc finge 39.7 17 0.00037 28.4 1.4 38 114-151 7-46 (69)
188 COG5432 RAD18 RING-finger-cont 38.9 15 0.00033 37.2 1.2 32 277-315 26-59 (391)
189 KOG2114 Vacuolar assembly/sort 38.8 18 0.0004 41.8 2.0 40 117-170 841-880 (933)
190 KOG3039 Uncharacterized conser 38.1 18 0.0004 35.8 1.6 37 117-155 44-80 (303)
191 KOG1571 Predicted E3 ubiquitin 37.5 16 0.00035 38.1 1.2 43 115-172 304-346 (355)
192 PF12677 DUF3797: Domain of un 37.5 28 0.00061 25.7 2.1 26 277-302 14-47 (49)
193 PRK12495 hypothetical protein; 37.2 24 0.00052 34.5 2.2 17 276-292 42-58 (226)
194 PF05290 Baculo_IE-1: Baculovi 36.9 21 0.00045 32.1 1.6 51 115-172 79-131 (140)
195 KOG0309 Conserved WD40 repeat- 36.9 24 0.00052 40.3 2.4 49 115-172 1027-1075(1081)
196 COG2051 RPS27A Ribosomal prote 36.9 34 0.00073 27.0 2.6 31 208-241 20-51 (67)
197 TIGR00686 phnA alkylphosphonat 36.6 28 0.00061 30.2 2.3 26 277-303 3-29 (109)
198 PF10446 DUF2457: Protein of u 36.4 19 0.00042 38.7 1.6 6 346-351 407-412 (458)
199 PRK11827 hypothetical protein; 36.3 29 0.00063 26.9 2.1 25 277-301 9-34 (60)
200 PRK14892 putative transcriptio 36.2 26 0.00055 30.1 2.0 27 276-302 21-51 (99)
201 PRK09710 lar restriction allev 36.2 32 0.00069 27.0 2.3 14 275-288 5-18 (64)
202 cd07621 BAR_SNX5_6 The Bin/Amp 35.9 4.4E+02 0.0095 26.0 11.7 60 436-495 156-215 (219)
203 KOG4362 Transcriptional regula 35.8 11 0.00024 42.9 -0.4 51 116-175 21-71 (684)
204 PF06827 zf-FPG_IleRS: Zinc fi 35.6 25 0.00054 22.9 1.5 24 277-300 2-28 (30)
205 PF04931 DNA_pol_phi: DNA poly 35.5 62 0.0013 38.1 5.8 20 68-87 764-783 (784)
206 KOG3053 Uncharacterized conser 35.5 27 0.00059 34.9 2.3 53 115-170 19-79 (293)
207 PLN02189 cellulose synthase 35.4 23 0.00051 42.2 2.2 59 209-295 36-95 (1040)
208 PHA02926 zinc finger-like prot 35.4 38 0.00083 33.3 3.3 35 233-287 196-230 (242)
209 PF12861 zf-Apc11: Anaphase-pr 35.3 16 0.00035 30.3 0.7 35 277-314 33-67 (85)
210 PF14149 YhfH: YhfH-like prote 35.1 3.5 7.5E-05 28.6 -2.7 26 274-299 11-37 (37)
211 PRK04023 DNA polymerase II lar 35.0 25 0.00054 41.7 2.3 31 274-310 624-660 (1121)
212 KOG2164 Predicted E3 ubiquitin 34.8 14 0.0003 40.4 0.3 28 276-310 186-215 (513)
213 PRK14811 formamidopyrimidine-D 33.7 29 0.00062 35.3 2.3 25 276-300 235-262 (269)
214 COG1594 RPB9 DNA-directed RNA 33.6 31 0.00068 30.2 2.2 25 277-303 3-32 (113)
215 PHA02929 N1R/p28-like protein; 33.1 18 0.00039 36.0 0.7 38 276-313 174-214 (238)
216 TIGR02300 FYDLN_acid conserved 33.0 25 0.00054 31.4 1.5 25 277-302 10-35 (129)
217 PF06906 DUF1272: Protein of u 32.9 15 0.00033 27.9 0.1 44 117-172 6-51 (57)
218 PF09026 CENP-B_dimeris: Centr 32.8 15 0.00032 31.1 0.0 9 54-62 52-60 (101)
219 COG0266 Nei Formamidopyrimidin 32.4 30 0.00066 35.1 2.2 25 276-300 245-272 (273)
220 cd07662 BAR_SNX6 The Bin/Amphi 32.3 5E+02 0.011 25.6 11.4 59 436-494 155-213 (218)
221 PF15290 Syntaphilin: Golgi-lo 32.1 2E+02 0.0043 29.3 7.7 24 466-489 119-142 (305)
222 KOG2906 RNA polymerase III sub 32.0 48 0.001 28.2 2.9 27 208-237 2-30 (105)
223 TIGR01206 lysW lysine biosynth 31.7 45 0.00098 25.3 2.5 27 209-238 4-32 (54)
224 KOG2417 Predicted G-protein co 31.5 4.3E+02 0.0094 28.0 10.2 14 386-399 227-240 (462)
225 TIGR00993 3a0901s04IAP86 chlor 31.3 64 0.0014 37.1 4.7 41 38-82 412-452 (763)
226 PF14446 Prok-RING_1: Prokaryo 30.8 39 0.00084 25.6 2.0 33 116-148 5-39 (54)
227 COG2888 Predicted Zn-ribbon RN 30.6 25 0.00055 27.1 1.0 6 278-283 29-34 (61)
228 PF04899 MbeD_MobD: MbeD/MobD 30.6 2.8E+02 0.0061 22.2 7.4 48 434-486 17-64 (70)
229 PRK01103 formamidopyrimidine/5 30.4 35 0.00075 34.7 2.3 25 276-300 245-272 (274)
230 KOG4684 Uncharacterized conser 30.4 50 0.0011 32.1 3.1 15 208-223 139-153 (275)
231 PF08792 A2L_zn_ribbon: A2L zi 30.3 46 0.001 22.5 2.1 12 276-287 3-14 (33)
232 TIGR00577 fpg formamidopyrimid 30.3 35 0.00076 34.7 2.3 24 276-299 245-271 (272)
233 COG5109 Uncharacterized conser 30.2 45 0.00098 34.3 3.0 51 115-172 335-386 (396)
234 PRK14810 formamidopyrimidine-D 29.9 35 0.00076 34.7 2.2 25 276-300 244-271 (272)
235 cd07622 BAR_SNX4 The Bin/Amphi 29.9 5.2E+02 0.011 25.0 13.2 95 381-492 97-194 (201)
236 PF14471 DUF4428: Domain of un 29.5 37 0.0008 25.3 1.7 30 118-148 1-30 (51)
237 PRK13945 formamidopyrimidine-D 29.4 36 0.00079 34.7 2.2 25 276-300 254-281 (282)
238 PRK10445 endonuclease VIII; Pr 29.2 38 0.00082 34.2 2.3 25 276-300 235-262 (263)
239 COG2178 Predicted RNA-binding 29.2 5.4E+02 0.012 25.0 10.9 50 353-402 38-90 (204)
240 PF13453 zf-TFIIB: Transcripti 29.2 33 0.00071 24.1 1.3 29 278-311 1-29 (41)
241 PLN02638 cellulose synthase A 29.1 31 0.00068 41.3 1.9 56 215-295 22-78 (1079)
242 COG1623 Predicted nucleic-acid 28.7 1.8E+02 0.0039 29.9 6.8 31 334-364 151-181 (349)
243 PF09723 Zn-ribbon_8: Zinc rib 28.0 64 0.0014 22.9 2.7 12 277-288 27-39 (42)
244 PF10122 Mu-like_Com: Mu-like 27.4 25 0.00054 26.3 0.4 25 277-301 5-32 (51)
245 smart00659 RPOLCX RNA polymera 27.3 49 0.0011 23.9 2.0 10 277-286 20-29 (44)
246 PF05715 zf-piccolo: Piccolo Z 27.3 24 0.00053 27.1 0.4 34 277-310 3-39 (61)
247 COG3813 Uncharacterized protei 27.0 34 0.00074 27.3 1.2 43 118-172 7-51 (84)
248 PRK08115 ribonucleotide-diphos 27.0 30 0.00066 40.7 1.3 24 277-302 828-853 (858)
249 KOG0943 Predicted ubiquitin-pr 26.6 38 0.00081 40.9 1.9 14 280-293 2282-2295(3015)
250 PF08746 zf-RING-like: RING-li 26.6 40 0.00086 24.1 1.4 41 119-165 1-42 (43)
251 PRK00415 rps27e 30S ribosomal 26.6 62 0.0014 25.0 2.5 31 208-241 12-43 (59)
252 PF01428 zf-AN1: AN1-like Zinc 26.5 31 0.00068 24.6 0.8 25 214-244 4-29 (43)
253 PF06844 DUF1244: Protein of u 26.1 38 0.00083 26.7 1.3 17 139-155 11-27 (68)
254 TIGR02159 PA_CoA_Oxy4 phenylac 26.1 30 0.00066 31.8 0.9 95 48-148 41-140 (146)
255 PLN02436 cellulose synthase A 26.0 43 0.00093 40.2 2.2 56 215-295 41-97 (1094)
256 PRK09521 exosome complex RNA-b 26.0 45 0.00097 31.9 2.1 24 278-302 151-175 (189)
257 TIGR00373 conserved hypothetic 25.9 83 0.0018 29.2 3.8 32 203-237 105-137 (158)
258 COG5194 APC11 Component of SCF 25.8 52 0.0011 27.0 2.0 35 117-151 32-69 (88)
259 COG2816 NPY1 NTP pyrophosphohy 25.7 63 0.0014 32.9 3.1 35 268-303 104-139 (279)
260 COG5236 Uncharacterized conser 25.4 42 0.00092 34.9 1.8 32 114-147 59-90 (493)
261 PF02891 zf-MIZ: MIZ/SP-RING z 25.3 62 0.0013 23.9 2.3 47 117-170 3-49 (50)
262 PF15616 TerY-C: TerY-C metal 25.2 66 0.0014 29.0 2.8 21 214-241 81-101 (131)
263 PF05605 zf-Di19: Drought indu 25.1 91 0.002 23.2 3.2 45 116-177 2-46 (54)
264 PLN02915 cellulose synthase A 24.8 44 0.00094 40.0 2.0 56 215-295 20-76 (1044)
265 smart00531 TFIIE Transcription 24.6 99 0.0022 28.2 4.0 18 57-74 20-37 (147)
266 PF06044 DRP: Dam-replacing fa 24.6 45 0.00098 33.1 1.8 22 266-288 22-44 (254)
267 PTZ00083 40S ribosomal protein 24.4 79 0.0017 26.2 2.8 35 208-245 36-71 (85)
268 PF15616 TerY-C: TerY-C metal 24.3 44 0.00096 30.1 1.5 36 275-310 76-114 (131)
269 KOG2932 E3 ubiquitin ligase in 24.2 35 0.00076 35.0 1.0 28 276-310 90-120 (389)
270 smart00064 FYVE Protein presen 23.8 31 0.00067 26.8 0.4 36 116-151 10-47 (68)
271 PF00098 zf-CCHC: Zinc knuckle 23.8 50 0.0011 19.0 1.2 16 238-253 2-17 (18)
272 PF14353 CpXC: CpXC protein 23.6 36 0.00079 30.2 0.9 50 161-223 2-51 (128)
273 PF14319 Zn_Tnp_IS91: Transpos 23.5 41 0.00088 29.4 1.2 28 207-245 42-69 (111)
274 KOG4759 Ribosome recycling fac 23.5 7.3E+02 0.016 25.1 9.9 67 431-497 196-262 (263)
275 PRK03564 formate dehydrogenase 23.2 68 0.0015 33.3 2.9 34 277-310 188-235 (309)
276 PF07503 zf-HYPF: HypF finger; 23.2 52 0.0011 22.6 1.4 30 140-171 1-30 (35)
277 PRK06266 transcription initiat 23.0 99 0.0022 29.4 3.8 32 203-237 113-145 (178)
278 KOG0943 Predicted ubiquitin-pr 22.9 43 0.00093 40.4 1.5 19 435-453 2418-2436(3015)
279 PF15358 TSKS: Testis-specific 22.8 5.8E+02 0.013 27.5 9.4 91 338-457 122-214 (558)
280 PLN02400 cellulose synthase 22.6 70 0.0015 38.6 3.1 56 215-295 41-97 (1085)
281 PF01667 Ribosomal_S27e: Ribos 22.6 76 0.0016 24.2 2.3 33 208-243 8-41 (55)
282 KOG0824 Predicted E3 ubiquitin 22.5 31 0.00067 35.3 0.2 26 276-310 7-36 (324)
283 TIGR02443 conserved hypothetic 22.4 75 0.0016 24.5 2.2 26 277-302 10-40 (59)
284 PF03854 zf-P11: P-11 zinc fin 22.2 38 0.00082 25.0 0.6 44 117-174 3-47 (50)
285 KOG4739 Uncharacterized protei 22.1 50 0.0011 32.8 1.5 16 233-248 22-37 (233)
286 PF03833 PolC_DP2: DNA polymer 22.0 30 0.00065 40.3 0.0 13 277-289 681-693 (900)
287 PF03615 GCM: GCM motif protei 21.6 77 0.0017 28.5 2.5 20 277-302 83-106 (143)
288 cd07630 BAR_SNX_like The Bin/A 21.6 7.3E+02 0.016 23.9 13.4 62 431-492 132-193 (198)
289 PF08271 TF_Zn_Ribbon: TFIIB z 21.6 74 0.0016 22.5 2.0 26 209-237 2-28 (43)
290 KOG1464 COP9 signalosome, subu 21.3 51 0.0011 33.6 1.4 12 1-12 1-12 (440)
291 PRK00420 hypothetical protein; 21.2 1.9E+02 0.004 25.5 4.7 43 187-244 6-48 (112)
292 COG1096 Predicted RNA-binding 21.1 59 0.0013 31.1 1.8 23 277-301 150-173 (188)
293 PLN00209 ribosomal protein S27 21.1 88 0.0019 26.0 2.5 34 208-244 37-71 (86)
294 PF14319 Zn_Tnp_IS91: Transpos 21.1 1.8E+02 0.0039 25.3 4.7 34 228-261 41-77 (111)
295 PF08580 KAR9: Yeast cortical 21.0 4.1E+02 0.0088 30.9 8.8 23 470-492 312-334 (683)
296 KOG0825 PHD Zn-finger protein 21.0 65 0.0014 37.2 2.3 48 116-173 123-171 (1134)
297 PF06044 DRP: Dam-replacing fa 20.9 67 0.0015 32.0 2.2 41 194-240 21-65 (254)
298 PF03604 DNA_RNApol_7kD: DNA d 20.8 47 0.001 22.3 0.8 10 277-286 18-27 (32)
299 COG3024 Uncharacterized protei 20.8 48 0.001 26.0 0.9 14 275-288 6-19 (65)
300 PF06056 Terminase_5: Putative 20.7 1.3E+02 0.0028 23.0 3.3 29 54-82 15-43 (58)
301 PF14569 zf-UDP: Zinc-binding 20.6 1.1E+02 0.0025 24.9 3.0 48 115-171 8-60 (80)
302 PF07800 DUF1644: Protein of u 20.4 95 0.0021 28.9 2.9 36 116-153 2-50 (162)
303 cd00065 FYVE FYVE domain; Zinc 20.3 52 0.0011 24.4 1.1 35 117-151 3-39 (57)
304 PHA02325 hypothetical protein 20.3 48 0.001 25.9 0.8 11 275-285 2-12 (72)
305 PF05129 Elf1: Transcription e 20.2 49 0.0011 27.2 0.9 28 276-303 22-56 (81)
306 PRK12775 putative trifunctiona 20.2 8.3E+02 0.018 29.8 11.6 15 276-290 796-810 (1006)
307 KOG3800 Predicted E3 ubiquitin 20.2 57 0.0012 33.3 1.5 52 209-289 2-53 (300)
308 PRK12286 rpmF 50S ribosomal pr 20.2 66 0.0014 24.6 1.5 13 275-287 26-38 (57)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-69 Score=580.84 Aligned_cols=429 Identities=40% Similarity=0.769 Sum_probs=381.3
Q ss_pred eeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCCCCCCCcccccccc
Q 008947 41 VITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPMLPLSSTVMCD 120 (548)
Q Consensus 41 vlt~~~l~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~C~ 120 (548)
|+|.+++...|.++|.+|+++|++++.+|++||.||.|+.+++++.|++ +.+..+..+|+.+.. ......+|.
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~------~~~~~~~c~ 74 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWP------KKKGDVQCG 74 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccC------CCCccccCC
Confidence 6899999999999999999999999999999999999999999999996 556777778865543 223468999
Q ss_pred cccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhccCCh-hHHHHHHHHHHHH
Q 008947 121 ICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHP-NLAEKFERFLLES 199 (548)
Q Consensus 121 IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~-e~~~ky~~~l~~~ 199 (548)
||++.++. .+..+.|||.||..||..|+..+|.+|....|+||..+|.+.+....|..+++ + +...+|.++++++
T Consensus 75 ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s---~~~~~~ky~~~i~~s 150 (444)
T KOG1815|consen 75 ICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVS---DKEDKEKYQRYILRS 150 (444)
T ss_pred cccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecC---CHHHHHHHHHHHHHH
Confidence 99999865 67888999999999999999999998875559999999999999999999998 4 5899999999999
Q ss_pred hhhcCcccccCCCCCCCCceEEeccCceeeeeccCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCC
Q 008947 200 FIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPC 279 (548)
Q Consensus 200 ~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~C 279 (548)
||+.+..++|||+ |+|++++.........|.|.||+.|||.|+.+||.|++|..+..|.++..+++++.+||..|+++|
T Consensus 151 yve~~~~lkwCP~-~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~C 229 (444)
T KOG1815|consen 151 YVEDNVPLKWCPA-PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKEC 229 (444)
T ss_pred HHhcCCccccCCC-CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccC
Confidence 9999999999996 999999997555556799999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeecCCCCceEec---ccccccccccccccCCCCccccCCccCCCCccchHHH-HHHHHHHHhHHHHHHHHHHH
Q 008947 280 PKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKK-TERAKRELYRYMHYHNRYKA 355 (548)
Q Consensus 280 PkC~~~IEKn~GCnhMtC~---C~~~FCw~C~~~~~~~H~w~~~~g~~C~~y~~~~~~~-~~~~k~~l~ry~~y~~r~~~ 355 (548)
|+|..+|||++|||||+|. |++.|||+|++.|. +|+.+. ++.||+|..+.... +..++..+.||.|||+||+.
T Consensus 230 P~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~-~h~~~~--~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~~ 306 (444)
T KOG1815|consen 230 PKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS-DHGSST--GYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWME 306 (444)
T ss_pred CCcccchhccCCccccccccCCcCCeeceeeecccc-cccccc--eeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHHh
Confidence 9999999999999999994 99999999988875 454433 79999999877655 77888999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHH-HHHhhhh-hccccchhHHHHHHHHHHHHhHhhhccceeeeeccCccccccccChHHHHHhH
Q 008947 356 HTDSFKLESKLKETVLEK-VSISEER-ESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQ 433 (548)
Q Consensus 356 h~~s~k~e~~l~~~i~~k-~~~~~~~-~~~~~~~~~l~~a~~~l~~~R~~L~~sy~~~yy~~~~~~~~~~~~~~e~~~~~ 433 (548)
|..+++++..+...+++. ...+... ...+.+++|+.+|+.+|+++|+||+|||+|+||+..+ .+.
T Consensus 307 ~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~~-------------~~~ 373 (444)
T KOG1815|consen 307 HQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSEN-------------NKR 373 (444)
T ss_pred hhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhccc-------------chh
Confidence 999999998776666543 3333322 2347799999999999999999999999999999721 345
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 008947 434 HLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLG 497 (548)
Q Consensus 434 ~lfe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~ 497 (548)
++||++|++||..+|.|+..++.++...+..++..+|+++.+++.++++++.+++..++++|..
T Consensus 374 ~~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 437 (444)
T KOG1815|consen 374 NLFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLED 437 (444)
T ss_pred hhhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccchhhhhHHHHHHHHHHhcccc
Confidence 8999999999999999999999988877778899999999999999999999999999998874
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6e-35 Score=306.39 Aligned_cols=269 Identities=29% Similarity=0.567 Sum_probs=204.5
Q ss_pred HHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCC-----------CCC---CCccccccccccccccc-ccCce
Q 008947 68 HARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDA-----------DPM---LPLSSTVMCDICMEEVA-GDKAT 132 (548)
Q Consensus 68 ~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~-----------~~~---~~~~~~~~C~IC~e~~~-~~~~~ 132 (548)
.+......+.|+...|.+.+.. ....+.....+.++... ... .......+|.||+.+.+ .+.++
T Consensus 85 v~~~~~~~~~~~~~~l~~~v~~-~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s~~~~~~~~~~C~iC~~e~~~~~~~f 163 (384)
T KOG1812|consen 85 VAGREKPEQHRKIVLLVELVQR-IREQLTSSEPILVPKNADIKFAYKLAREAIVSQLPSKLPKEECGICFVEDPEAEDMF 163 (384)
T ss_pred HhhhhhHHHHHHHHHHHHHHHH-HHHHhhcccceecccchhhHHHHHHHHHhhccccccccccccCccCccccccHhhhH
Confidence 4555555666777777776642 23333333333322210 000 11123578999995433 33444
Q ss_pred e-cCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhccCChhHHHHHHHHHHHHhhhcCcccccCC
Q 008947 133 K-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCP 211 (548)
Q Consensus 133 ~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l~~~~v~~~~~~~~CP 211 (548)
. ..|+|.||.+||++|+..+...| ..++||..+|+..++.+....+|+ +.+.++|++++.+.++.....+ +||
T Consensus 164 ~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt---~kl~e~~e~~~~e~~i~~~~~~-ycp 237 (384)
T KOG1812|consen 164 SVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLT---PKLREMWEQRLKEEVIPSLDRV-YCP 237 (384)
T ss_pred HHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcC---HHHHHHHHHHHHHHhhhhhhcc-cCC
Confidence 4 58999999999999999984444 589999999999999999999999 8999999999999999988888 999
Q ss_pred CCCCCCceEEecc----Cceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcce
Q 008947 212 STPHCGNAIRVEE----VEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPV 286 (548)
Q Consensus 212 ~~p~C~~~i~~~~----~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~I 286 (548)
.|+|...+.... .......|+ |+..||..|+.+||++.+|..+++|......++.+++++..+|+.||+|+..|
T Consensus 238 -~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~i 316 (384)
T KOG1812|consen 238 -YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMI 316 (384)
T ss_pred -CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceee
Confidence 699988776433 223345676 99999999999999999999999999887888889999999999999999999
Q ss_pred eecCCCCceEecccccccccccccccCCCCccccCCccCCCCccchHHHHHHHHHHHhHHHHHHHHHHHhhhHHHHH
Q 008947 287 EKNGGCNLVSCICGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKKTERAKRELYRYMHYHNRYKAHTDSFKLE 363 (548)
Q Consensus 287 EKn~GCnhMtC~C~~~FCw~C~~~~~~~H~w~~~~g~~C~~y~~~~~~~~~~~k~~l~ry~~y~~r~~~h~~s~k~e 363 (548)
|+++|||||+|+||++|||.|+++|.... +.-+.|.++++. ++|+.++.+|.....++
T Consensus 317 e~~~GCnhm~CrC~~~fcy~C~~~~~~~~----~~~~~~~r~~~~---------------~~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 317 ELSEGCNHMTCRCGHQFCYMCGGDWKTHN----GECYECCRYKES---------------THYFEDDENHDKSIQLE 374 (384)
T ss_pred eecCCcceEEeeccccchhhcCcchhhCC----ccccCccccccc---------------ccccccccccccccccc
Confidence 99999999999999999999999964211 112566676654 67888887777665544
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-34 Score=290.11 Aligned_cols=203 Identities=27% Similarity=0.673 Sum_probs=173.8
Q ss_pred cccccccccccccc-cCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhccCChhHHHHHH
Q 008947 115 STVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFE 193 (548)
Q Consensus 115 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~ 193 (548)
..+.|.|||+.... ..+..++|+|.||+.|++.|++..|++|.+..++||.++|+...++..++.++. .++++||+
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 259 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVG---DELFARYE 259 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHH---HHHHHHHH
Confidence 56899999999765 566778999999999999999999999999999999999999999999999999 99999999
Q ss_pred HHHHHHhhhcCcccccCCCCCCCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhh--------HHHHH----
Q 008947 194 RFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMW--------DLWAK---- 260 (548)
Q Consensus 194 ~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~--------~~w~~---- 260 (548)
+.++++.++...++++|| .+.|...+. .+.....+.|+ |..+||+.|+..||...+|... ..|..
T Consensus 260 ~l~lqk~l~~msdv~yCP-r~~Cq~p~~-~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCP-RACCQLPVK-QDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCC-hhhccCccc-cCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 999999999999999999 589999884 44444568997 9999999999999999899643 12221
Q ss_pred ---------------hhhchHHHHHHHHhCCcCCCCCCcceeecCCCCceEe-cccccccccccccccCCCCccccCC
Q 008947 261 ---------------KCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTWSRIAG 322 (548)
Q Consensus 261 ---------------~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~~~H~w~~~~g 322 (548)
...++-.+..|+..|.|+||+|+++|||++|||||+| .|++.|||+|+....+...|.|+.+
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e 415 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSE 415 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcC
Confidence 1112334568999999999999999999999999999 6999999999988766655665554
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=1e-24 Score=213.09 Aligned_cols=194 Identities=29% Similarity=0.669 Sum_probs=146.9
Q ss_pred cccccccccccccccccCceecCCC--CccchhhHHHHHHhhhccCCc-------cceecCccccccccchH-HHHHhhc
Q 008947 113 LSSTVMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQS-------KRIRCMAHKCNAICDEA-VVRNLVS 182 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~i~~g~~-------~~i~CP~~~C~~~i~~~-~i~~ll~ 182 (548)
+....+|..|.+.- +.+..++|. |..|.+|++.|..+.+++.+. ..+.||. +|...+-.+ .--++|.
T Consensus 218 N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg 294 (446)
T KOG0006|consen 218 NSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 45678999998874 244566888 999999999999999987763 2356665 566543222 2235677
Q ss_pred cCChhHHHHHHHHHHHHhhhcCcccccCCCCCCCCceEEeccCceeeeecc--CCCccccCcCccCCCC-C---------
Q 008947 183 KKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA--CGAQFCFSCLSEAHSP-C--------- 250 (548)
Q Consensus 183 ~~~~e~~~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--Cg~~fC~~C~~~~H~p-~--------- 250 (548)
.+.+.+|+++..+.+|.....+ -|| .|+||..+.++++. ..|+|+ ||..||..|++.+|.+ +
T Consensus 295 ---~e~Y~rYQr~atEe~vlq~gGV-lCP-~pgCG~gll~EPD~-rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t 368 (446)
T KOG0006|consen 295 ---EEQYNRYQRYATEECVLQMGGV-LCP-RPGCGAGLLPEPDQ-RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGT 368 (446)
T ss_pred ---hhHHHHHHHhhhhhheeecCCE-ecC-CCCCCcccccCCCC-CcccCCCCchhHhHHHHHhhhccccceeeeccccc
Confidence 8999999999999999888765 899 69999998877644 468995 9999999999999985 1
Q ss_pred -Cchhh--HHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCCceEe-c--ccccccccccccccCCC
Q 008947 251 -SCSMW--DLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-I--CGQAFCWLCGGATGRDH 315 (548)
Q Consensus 251 -~C~~~--~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC-~--C~~~FCw~C~~~~~~~H 315 (548)
+|... .+-....+-+..+..-|+..||+||+|+.|.||||||+||.| + ||.+|||.|+-.|.+.-
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhh
Confidence 24310 000011122344455588899999999999999999999999 4 99999999999987643
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.23 E-value=1.3e-11 Score=96.97 Aligned_cols=62 Identities=53% Similarity=1.095 Sum_probs=55.1
Q ss_pred HHHHHHHHHHhhhcCcccccCCCCCCCCceEEec-cCceeeeecc-CCCccccCcCccCCCCCCc
Q 008947 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE-EVEVCEVECA-CGAQFCFSCLSEAHSPCSC 252 (548)
Q Consensus 190 ~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C 252 (548)
++|++++++++|+.++.++||| +|+|+.++... +.....|.|+ |+..||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP-~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCP-APDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCC-CCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4789999999999988999999 69999999876 3455679995 9999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.11 E-value=1.4e-11 Score=96.72 Aligned_cols=62 Identities=35% Similarity=0.960 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhhhcCcccccCCCCCCCCceEEeccCcee-eeecc-CCCccccCcCccCCCCCCc
Q 008947 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVC-EVECA-CGAQFCFSCLSEAHSPCSC 252 (548)
Q Consensus 190 ~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-Cg~~fC~~C~~~~H~p~~C 252 (548)
++|++++++.+++.++.++||| +|+|+.++...+.... .++|+ |++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp-~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCP-NPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--T-TSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCC-CCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 5788999999999888999999 6999999997765444 48998 9999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.51 E-value=5e-08 Score=70.06 Aligned_cols=41 Identities=24% Similarity=0.748 Sum_probs=30.1
Q ss_pred cccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
|+||++.+ .++++++|||.||..|+..++...-.. .+.||.
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~----~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGS----GFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSS----T---SS
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCc----CCCCcC
Confidence 89999998 489999999999999999999763322 278886
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.12 E-value=1.3e-06 Score=63.37 Aligned_cols=40 Identities=38% Similarity=0.836 Sum_probs=32.9
Q ss_pred cccccccccc-ccCceecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 118 MCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 118 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
+|+||++++. ...++.++|||.||.+|+..|+... .+||.
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 6999999985 4667788999999999999999762 27887
No 9
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.11 E-value=1.5e-06 Score=61.29 Aligned_cols=37 Identities=30% Similarity=0.872 Sum_probs=29.1
Q ss_pred cccccccccccCc-eecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 119 CDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 119 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
|+||++.+. ++ +.++|||.||.+||..|+... .+||.
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 899999864 45 678999999999999998762 47876
No 10
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.08 E-value=2.1e-06 Score=61.12 Aligned_cols=39 Identities=31% Similarity=0.867 Sum_probs=32.0
Q ss_pred cccccccccccCce-ecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 119 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 119 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
|+||++.+. .+. .++|||.||..||.+++.. . ..++||.
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 899999874 444 7899999999999999997 2 3467886
No 11
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.06 E-value=4.8e-06 Score=65.05 Aligned_cols=38 Identities=37% Similarity=0.872 Sum_probs=34.3
Q ss_pred CCcCCC--CCCcceeecC--CCCceEe-ccccccccccccccc
Q 008947 275 HTKPCP--KCHKPVEKNG--GCNLVSC-ICGQAFCWLCGGATG 312 (548)
Q Consensus 275 ~tK~CP--kC~~~IEKn~--GCnhMtC-~C~~~FCw~C~~~~~ 312 (548)
+.+.|| +|+..|+..+ |.++|+| .|++.|||.|+.+||
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 568899 9999999964 9999999 799999999999974
No 12
>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=97.99 E-value=2.8e-06 Score=66.38 Aligned_cols=38 Identities=42% Similarity=1.069 Sum_probs=28.6
Q ss_pred CCcCCCC--CCcceeecCCCCc--eEec-cccccccccccccc
Q 008947 275 HTKPCPK--CHKPVEKNGGCNL--VSCI-CGQAFCWLCGGATG 312 (548)
Q Consensus 275 ~tK~CPk--C~~~IEKn~GCnh--MtC~-C~~~FCw~C~~~~~ 312 (548)
+.+.||+ |...|++..|.++ |+|. |++.|||.|+++||
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 3589988 9999999999999 9996 99999999999974
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.93 E-value=4.6e-06 Score=77.07 Aligned_cols=54 Identities=24% Similarity=0.637 Sum_probs=42.4
Q ss_pred cccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHH
Q 008947 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~ 176 (548)
....+.|+||++.+....+++..|||.||..|++.-+.. ..+||. |...++..+
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~ 181 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQ 181 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhh
Confidence 345689999999998777788999999999999987764 248999 555555443
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.92 E-value=6.8e-06 Score=77.87 Aligned_cols=65 Identities=23% Similarity=0.532 Sum_probs=47.5
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhcc--------CCccceecCccccccccchHHHHHhhc
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE--------GQSKRIRCMAHKCNAICDEAVVRNLVS 182 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~--------g~~~~i~CP~~~C~~~i~~~~i~~ll~ 182 (548)
.+.++|+||++.+ .+++.++|||.||..|+..|+...-.. ......+||. |...+....+..+..
T Consensus 16 ~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 3568999999986 477888999999999999997642110 0113579999 999887665554443
No 15
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.91 E-value=5.8e-06 Score=59.55 Aligned_cols=41 Identities=32% Similarity=0.783 Sum_probs=22.9
Q ss_pred cccccccccc--cCceecCCCCccchhhHHHHHHhhhccCCccceecC
Q 008947 119 CDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCM 164 (548)
Q Consensus 119 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP 164 (548)
|+||.+ +.. ..+..|+|||.||++|+...+.... ...++||
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 632 2367789999999999999988533 1358887
No 16
>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=97.73 E-value=2.4e-05 Score=55.87 Aligned_cols=44 Identities=32% Similarity=0.851 Sum_probs=32.7
Q ss_pred ccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 118 MCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
+|+||++.+. ......+|||.||..|+..|+.. + ..+||. |+..
T Consensus 1 ~C~iC~~~~~-~~~~~~~C~H~~c~~C~~~~~~~----~---~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR-EPVVLLPCGHVFCRSCIDKWLKS----G---KNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh-CceEecCCCChhcHHHHHHHHHh----C---cCCCCC--CCCc
Confidence 5999999872 23334469999999999999875 2 357987 7653
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.73 E-value=1.8e-05 Score=57.45 Aligned_cols=42 Identities=31% Similarity=0.886 Sum_probs=33.3
Q ss_pred cccccccccc-ccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccc
Q 008947 118 MCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (548)
Q Consensus 118 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 169 (548)
.|+||++.+. ...+..++|||.||..|+.... . ..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-----~---~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-----G---KSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-----C---CCCCCcC--CC
Confidence 4999999983 3456677999999999999987 1 3578998 64
No 18
>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=97.70 E-value=2.6e-05 Score=58.12 Aligned_cols=46 Identities=26% Similarity=0.711 Sum_probs=36.0
Q ss_pred ccccccccccccccCceecCCCCc-cchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
...|.||++.. .++..++|||. ||..|+..++.. ..+||. |...+.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~--------~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR--------KKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT--------TSBBTT--TTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc--------CCCCCc--CChhhc
Confidence 46899999985 36777899999 999999999882 358998 887653
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.53 E-value=3.6e-05 Score=74.31 Aligned_cols=60 Identities=25% Similarity=0.500 Sum_probs=46.5
Q ss_pred cccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhh
Q 008947 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLV 181 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll 181 (548)
....|+|.||++.. .+++...|||.||-.|+-+|+..+.+. -.||. |+..+..+.+--|.
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeee
Confidence 34679999999984 578888999999999999999885532 45888 88877766544333
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.45 E-value=8.7e-05 Score=50.97 Aligned_cols=30 Identities=37% Similarity=1.027 Sum_probs=26.3
Q ss_pred cccccccccccCceecCCCCccchhhHHHHHH
Q 008947 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFI 150 (548)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~ 150 (548)
|+||++.. ..+..++|||.||..|+..|+.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH
Confidence 78999883 4677889999999999999987
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=97.39 E-value=0.00013 Score=56.79 Aligned_cols=47 Identities=9% Similarity=0.164 Sum_probs=38.0
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
+.|+||.+.+. +++.++|||.||+.|+..|+.. . ..||. |+..++..
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~~---~-----~~cP~--~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLLS---H-----GTDPV--TGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHHH---C-----CCCCC--CcCCCChh
Confidence 67999999864 6888899999999999999975 1 36888 66666543
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=5.9e-05 Score=80.32 Aligned_cols=60 Identities=20% Similarity=0.503 Sum_probs=46.6
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhc
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 182 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~ 182 (548)
...||||++..+ -+..+.|||.||-.|+-+||...... .+..||. |...+....+..+..
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 678999999853 44556799999999999999987322 3578999 998887766655544
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=97.32 E-value=0.00012 Score=70.28 Aligned_cols=56 Identities=27% Similarity=0.538 Sum_probs=39.1
Q ss_pred ccccccccccccccc-----ccC--ceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 113 LSSTVMCDICMEEVA-----GDK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~-----~~~--~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
.+...+|+||++..- ... ....+|+|.||..|+..|-..+-..| ..-.||. |...+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f 229 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRF 229 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Cccee
Confidence 345689999999852 111 12339999999999999998753322 2357999 88754
No 24
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=0.0001 Score=73.34 Aligned_cols=50 Identities=28% Similarity=0.652 Sum_probs=41.3
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHH
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~ 176 (548)
....|.+|++.. .++..++|||.||..|+.+|...+- .||. |...+.+..
T Consensus 238 a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~psk 287 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSK 287 (293)
T ss_pred CCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcc
Confidence 458899999985 4788889999999999999998743 3998 988776654
No 25
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=0.00013 Score=73.75 Aligned_cols=44 Identities=30% Similarity=0.828 Sum_probs=37.2
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
+.+.|+||++.+. .+..++|||.||..|+...+. ..+.||. |..
T Consensus 12 ~~~~C~iC~~~~~--~p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFR--EPVLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP 55 (386)
T ss_pred ccccChhhHHHhh--cCccccccchHhHHHHHHhcC--------CCcCCcc--cCC
Confidence 5689999999985 457779999999999999998 2489998 773
No 26
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.24 E-value=0.00019 Score=70.91 Aligned_cols=50 Identities=28% Similarity=0.569 Sum_probs=36.6
Q ss_pred ccccccccccccccccC------ceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 114 SSTVMCDICMEEVAGDK------ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
+...+|+||++.+.... .+..+|+|.||..|+..|+.. ...||. |...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 34579999999864322 234589999999999998753 237998 887543
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=97.18 E-value=0.00024 Score=75.18 Aligned_cols=50 Identities=24% Similarity=0.583 Sum_probs=39.9
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
...+.|+||.+.+. .++.++|||.||..|+..|+... ..||. |...+...
T Consensus 24 e~~l~C~IC~d~~~--~PvitpCgH~FCs~CI~~~l~~~--------~~CP~--Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFD--VPVLTSCSHTFCSLCIRRCLSNQ--------PKCPL--CRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhh--CccCCCCCCchhHHHHHHHHhCC--------CCCCC--CCCccccc
Confidence 35689999999874 66778999999999999998641 37998 88766543
No 28
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.10 E-value=0.0032 Score=65.57 Aligned_cols=35 Identities=17% Similarity=0.555 Sum_probs=29.3
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHh
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~ 151 (548)
+...|+||..-+ .+++.|+|+|..|+.|-..-+.+
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhccc
Confidence 457899999877 48899999999999998865543
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.89 E-value=0.00066 Score=68.63 Aligned_cols=63 Identities=22% Similarity=0.582 Sum_probs=48.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHH--hhccCChhHHHHH
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRN--LVSKKHPNLAEKF 192 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~--ll~~~~~e~~~ky 192 (548)
..+-|.||++-|. -+...+|+|.||.-|++.|+.. ...||. |...+.+..++. +| .++++-|
T Consensus 22 ~lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il----~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRIL----DEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHhc--CceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHH----HHHHHHH
Confidence 4578999999984 4566789999999999999985 357998 998888877653 33 3666665
Q ss_pred H
Q 008947 193 E 193 (548)
Q Consensus 193 ~ 193 (548)
.
T Consensus 86 ~ 86 (442)
T KOG0287|consen 86 N 86 (442)
T ss_pred H
Confidence 4
No 30
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.71 E-value=0.0011 Score=50.75 Aligned_cols=47 Identities=21% Similarity=0.486 Sum_probs=30.5
Q ss_pred cccccccccccccccCce-ecCCCCccchhhHHHHHHhhhccCCccceecCccccc
Q 008947 115 STVMCDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 169 (548)
..+.|||....+. +|+ +..|||.|.++.+.+|+.. ...++||..||+
T Consensus 10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~------~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQR------NGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTT------TS-EE-SCCC-S
T ss_pred eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHh------cCCCCCCCCCCC
Confidence 3588999999874 554 4599999999999999921 246899999995
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.69 E-value=0.00084 Score=68.36 Aligned_cols=53 Identities=23% Similarity=0.491 Sum_probs=36.8
Q ss_pred cccccccccc-cccCce--ecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHH
Q 008947 117 VMCDICMEEV-AGDKAT--KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (548)
Q Consensus 117 ~~C~IC~e~~-~~~~~~--~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~ 178 (548)
..||||..+. ....+. ..+|||.||..|+...|.. | +..||. |...+....++
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~---~~~CP~--C~~~lrk~~fr 59 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G---SGSCPE--CDTPLRKNNFR 59 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C---CCCCCC--CCCccchhhcc
Confidence 5799999962 222221 1279999999999999742 2 358996 98877665443
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.35 E-value=0.00088 Score=74.87 Aligned_cols=55 Identities=25% Similarity=0.661 Sum_probs=44.0
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHh
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNL 180 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~l 180 (548)
...+||+|..- ..+.+...|||.||..|++..+.++- =+||. |+..+...+|..+
T Consensus 642 ~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 56899999944 35677789999999999999998743 47998 9988887766543
No 33
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.20 E-value=0.014 Score=42.01 Aligned_cols=40 Identities=23% Similarity=0.423 Sum_probs=34.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcC
Q 008947 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENG 91 (548)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~ 91 (548)
++.|.+.+++.|+++..|+.+|..++||++.-++.|++.+
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 3678899999999999999999999999999999999744
No 34
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.08 E-value=0.0015 Score=50.64 Aligned_cols=43 Identities=23% Similarity=0.733 Sum_probs=21.9
Q ss_pred ccccccccccccccCceec-CCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 116 TVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
...|++|.+.+ .+++.+ .|.|.||..|++..+.+ .||. |..+.
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~~----------~CPv--C~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIGS----------ECPV--CHTPA 50 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTTT----------B-SS--S--B-
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcCC----------CCCC--cCChH
Confidence 36799999986 467766 99999999999775432 4998 77654
No 35
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=96.04 E-value=0.34 Score=51.40 Aligned_cols=115 Identities=23% Similarity=0.445 Sum_probs=68.8
Q ss_pred eCHHHHHHHHHHHHHHHHHHcCCCHH--HHHHHHHHcCCChHH--HHHHHHhcCch--hhhhh---------hCCcccC-
Q 008947 42 ITRESLLAAQKEDLRRVMELLSLREH--HARTLLIHYRWDVEK--LLAVLVENGKE--SLFNE---------AGVTVID- 105 (548)
Q Consensus 42 lt~~~l~~~~~~~i~~v~~~l~i~~~--~a~~LL~~~~W~~~~--l~~~~~~~~~~--~~~~~---------~gl~~~~- 105 (548)
+|.-||+.-+--.+..|.++.-|..+ .-..+|+.|+=..+. .++.| +|+. .+-.+ +.+.-..
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~ef--NGk~Fn~le~e~Chll~V~~ve~~~s~d 163 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEF--NGKQFNSLEPEVCHLLYVDRVEVTESED 163 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHc--CCCcCCCCCccceeEEEEEEEEEEeccc
Confidence 78899999888888888888766532 345667777655443 23333 2221 11000 0111000
Q ss_pred -CCCCCCCcccccccccccccccccC--ceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 106 -DADPMLPLSSTVMCDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 106 -~~~~~~~~~~~~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
.+.++....+..+||||++-.+.+- ..+..|.|.|--.|+..|+. ..||. |..
T Consensus 164 ~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~ 219 (493)
T KOG0804|consen 164 GASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRY 219 (493)
T ss_pred CCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhh
Confidence 1111222345679999999875322 35568999999999998865 47887 654
No 36
>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=95.87 E-value=0.0048 Score=49.79 Aligned_cols=50 Identities=12% Similarity=0.109 Sum_probs=36.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
+.|.|+|+.+.+ .+++.+++||.|++.|+..|+.. ....||. |+..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcc
Confidence 468999999986 48899999999999999999987 2357888 56555543
No 37
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.70 E-value=0.0042 Score=66.22 Aligned_cols=55 Identities=20% Similarity=0.500 Sum_probs=43.8
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
.....|.+|-++- .+.+...|.|.||+-|+++|+.....+. .+.||. |...++.+
T Consensus 534 k~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 534 KGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred cCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 4568999999874 5777789999999999999998766543 389998 88766544
No 38
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.0073 Score=60.49 Aligned_cols=52 Identities=23% Similarity=0.536 Sum_probs=41.6
Q ss_pred ccccccccccccccc-cCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 114 SSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
....+|.||++.+.. +....+||.|.|...|+..|+.. ...+||. |...+|+
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP 373 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP 373 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 355899999999754 44566799999999999999874 3468998 9887764
No 39
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.38 E-value=0.011 Score=58.34 Aligned_cols=53 Identities=30% Similarity=0.567 Sum_probs=39.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
..+.|.||++.. ..+..++|||.||..|+-..|..+ ..-.||. |.+.+.+..|
T Consensus 214 ~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeeccc--CCcccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 367899999984 467788999999999999865432 1235998 8886655544
No 40
>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=95.35 E-value=0.01 Score=47.89 Aligned_cols=41 Identities=24% Similarity=0.486 Sum_probs=29.0
Q ss_pred cccccccccccc----------cCc-eecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 117 VMCDICMEEVAG----------DKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 117 ~~C~IC~e~~~~----------~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
..|.||++.+.. ..+ ....|||.|...|+..++... -.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC
Confidence 359999999821 122 334899999999999999652 27887
No 41
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.16 E-value=0.011 Score=61.31 Aligned_cols=45 Identities=29% Similarity=0.649 Sum_probs=36.8
Q ss_pred cccccccccccc-cCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 117 VMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 117 ~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
.+|.||+|++.. +....|+|+|.|...|+..|+... .-.||. |+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-------CccCCC--CCC
Confidence 799999999865 455678999999999999999873 236999 655
No 42
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.48 E-value=0.023 Score=45.45 Aligned_cols=57 Identities=25% Similarity=0.415 Sum_probs=26.8
Q ss_pred cccccccccccc-ccC-cee----cCCCCccchhhHHHHHHhhhccCCcc-ce--ecCccccccccch
Q 008947 116 TVMCDICMEEVA-GDK-ATK----MDCGHCFCNDCWTEHFIVKINEGQSK-RI--RCMAHKCNAICDE 174 (548)
Q Consensus 116 ~~~C~IC~e~~~-~~~-~~~----l~CgH~fC~~C~~~yl~~~i~~g~~~-~i--~CP~~~C~~~i~~ 174 (548)
...|+||+.... ... +.. ..|++.|...||.+||...-.....+ ++ .||. |...+..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 368999999753 222 211 26889999999999998766544322 32 6998 8887653
No 43
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.38 E-value=0.023 Score=56.55 Aligned_cols=47 Identities=28% Similarity=0.598 Sum_probs=36.3
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
...-|-||-+-+. -+...+|||.||.-|++.|+.++ .-||. |....-
T Consensus 24 s~lrC~IC~~~i~--ip~~TtCgHtFCslCIR~hL~~q--------p~CP~--Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRIS--IPCETTCGHTFCSLCIRRHLGTQ--------PFCPV--CREDPC 70 (391)
T ss_pred hHHHhhhhhheee--cceecccccchhHHHHHHHhcCC--------CCCcc--ccccHH
Confidence 4578999988764 45667999999999999999762 46887 766443
No 44
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.13 E-value=0.11 Score=52.47 Aligned_cols=145 Identities=22% Similarity=0.367 Sum_probs=78.5
Q ss_pred HHHHHcCCChHHHHHHHHhcCchhhhh-hhCCcccCCCCC----CCCcccccccccccccccccCceecCCCCccchhhH
Q 008947 71 TLLIHYRWDVEKLLAVLVENGKESLFN-EAGVTVIDDADP----MLPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCW 145 (548)
Q Consensus 71 ~LL~~~~W~~~~l~~~~~~~~~~~~~~-~~gl~~~~~~~~----~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~ 145 (548)
.-|.||+-=.+.-+++|-..+.++... .-|+.-+.+.-. ..|.....+|+ -.||-.||+.|+
T Consensus 285 ~e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~rkvtC~-------------~gCgf~FCR~C~ 351 (446)
T KOG0006|consen 285 KELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCE-------------GGCGFAFCRECK 351 (446)
T ss_pred HhhhhheecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCCCcccCC-------------CCchhHhHHHHH
Confidence 345688877788888887655554443 334433322110 01111112221 149999999999
Q ss_pred HHHHHhhhccCC--ccceecCccccccccchHHHHHhhccCChhHHHHHHHHHHHHhhhcCcccccCCCCCCCCceEEec
Q 008947 146 TEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE 223 (548)
Q Consensus 146 ~~yl~~~i~~g~--~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~ 223 (548)
..|-...-..+. +..- .|...+++.. ....+|+...-. ......+.|| .|..+....
T Consensus 352 e~yh~geC~~~~~as~t~-----tc~y~vde~~----------a~~arwd~as~~---TIk~tTkpCP---kChvptErn 410 (446)
T KOG0006|consen 352 EAYHEGECSAVFEASGTT-----TCAYRVDERA----------AEQARWDAASKE---TIKKTTKPCP---KCHVPTERN 410 (446)
T ss_pred hhhccccceeeecccccc-----ceeeecChhh----------hhhhhhhhhhhh---hhhhccCCCC---CccCccccC
Confidence 999654322211 0111 2443333321 122344433221 1223567888 797766543
Q ss_pred cCceeeeec--c-CCCccccCcCccCCCCC
Q 008947 224 EVEVCEVEC--A-CGAQFCFSCLSEAHSPC 250 (548)
Q Consensus 224 ~~~~~~v~C--~-Cg~~fC~~C~~~~H~p~ 250 (548)
.....+.| + ||..+||.|+.+|...+
T Consensus 411 -GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 411 -GGCMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred -CceEEeecCCCCCCceeEeccCChhhhhh
Confidence 33456789 3 99999999999987654
No 45
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.12 E-value=0.27 Score=51.62 Aligned_cols=38 Identities=37% Similarity=0.797 Sum_probs=34.5
Q ss_pred hCCcCCCC--CCcceeecCCCCceEe-cccccccccccccc
Q 008947 274 VHTKPCPK--CHKPVEKNGGCNLVSC-ICGQAFCWLCGGAT 311 (548)
Q Consensus 274 ~~tK~CPk--C~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~ 311 (548)
.+..-||+ |..|+-...|++-..| +|.+.||.+|...|
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~ 311 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTW 311 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhh
Confidence 45799999 9999977889999999 69999999999886
No 46
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.80 E-value=0.052 Score=53.94 Aligned_cols=50 Identities=22% Similarity=0.580 Sum_probs=37.5
Q ss_pred ccccccccccccccccCceec-CCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 114 SSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
+...+|++|-+.- ..|..+ +|||.||--|+..-+... ..+.||. |+..+.
T Consensus 237 t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred cCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 4568999998763 345555 699999999998876542 2479998 887665
No 47
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.66 E-value=0.033 Score=59.34 Aligned_cols=41 Identities=32% Similarity=0.754 Sum_probs=33.2
Q ss_pred cccccCCCCCCCCceEEeccCceeeeeccCCCccccCcCccCCCC
Q 008947 205 KMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSP 249 (548)
Q Consensus 205 ~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p 249 (548)
...+.|| .|+..|....+ ...++|.||+.||..|+.+|+..
T Consensus 304 ~~wr~Cp---kC~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 304 KRWRQCP---KCKFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred HhcCcCc---ccceeeeecCC-cceEEeeccccchhhcCcchhhC
Confidence 4577898 79988875544 56799999999999999888654
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.49 E-value=0.05 Score=39.99 Aligned_cols=44 Identities=30% Similarity=0.708 Sum_probs=21.2
Q ss_pred cccccccccccC--ceecCCCCccchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 119 CDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 119 C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
|++|.+++.... +.--+||+.+|+.||..-... .+ =+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~~----g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---EG----GRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S-----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---cC----CCCCC--CCCC
Confidence 789999874433 334489999999999987652 12 36988 7754
No 49
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=93.17 E-value=0.042 Score=35.10 Aligned_cols=23 Identities=39% Similarity=0.953 Sum_probs=16.2
Q ss_pred cCCCCCCcceeecCCCCceEec-ccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~~F 303 (548)
|.||.|+..|-.+. ..|. ||+.|
T Consensus 1 K~CP~C~~~V~~~~----~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESA----KFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhc----CcCCCCCCCC
Confidence 67999988886433 5674 77776
No 50
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.93 E-value=0.05 Score=54.75 Aligned_cols=53 Identities=21% Similarity=0.459 Sum_probs=40.4
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
...-+|+||+.+- ..++.|+|+|.||.-|++.-+.. +. -.|+. |...++...+
T Consensus 5 ~~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccC--CcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchh
Confidence 3456899999984 46789999999999999886543 22 35888 9888876654
No 51
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=92.79 E-value=0.069 Score=55.07 Aligned_cols=95 Identities=17% Similarity=0.251 Sum_probs=55.1
Q ss_pred CHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhh---hCCcccCCCCCCCCccccccccccccc-cccc----------C
Q 008947 65 REHHARTLLIHYRWDVEKLLAVLVENGKESLFNE---AGVTVIDDADPMLPLSSTVMCDICMEE-VAGD----------K 130 (548)
Q Consensus 65 ~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~---~gl~~~~~~~~~~~~~~~~~C~IC~e~-~~~~----------~ 130 (548)
+......|++.--|....|+.+-.+- -++.+. ..-..+.. ...........|.||.++ +.+. .
T Consensus 236 ~~r~Pi~l~r~~~t~~~AL~~~i~~~--~~~~r~~kdl~~~~~t~-t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~ 312 (491)
T COG5243 236 YVRVPIYLIRQMYTCFYALFRRIREH--ARFRRATKDLNAMYPTA-TEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMT 312 (491)
T ss_pred chhchHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhHHHhhcchh-hhhhhcCCCCeEEEecccccCCCCccCcccccCC
Confidence 33445667777777777776654321 011111 00000000 000112345789999999 4322 2
Q ss_pred ceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 131 ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 131 ~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
+..++|||.+...|++.|++.+ -.||. |+.++
T Consensus 313 pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ 344 (491)
T COG5243 313 PKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPV 344 (491)
T ss_pred cccccccceeeHHHHHHHHHhc--------cCCCc--ccCcc
Confidence 4688999999999999999852 37998 77653
No 52
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.26 E-value=0.19 Score=51.68 Aligned_cols=55 Identities=27% Similarity=0.666 Sum_probs=41.0
Q ss_pred ccccccccccccc----CceecCCCCccchhhHHHHHHhhhccCCccceecCccccccc--cchHHHHHh
Q 008947 117 VMCDICMEEVAGD----KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI--CDEAVVRNL 180 (548)
Q Consensus 117 ~~C~IC~e~~~~~----~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~--i~~~~i~~l 180 (548)
..|.||-++++.. -|..|.|||.+|..|....+.. ..+.||. |... ++...++.+
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSL 64 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhh
Confidence 5799999998754 2566789999999999988765 3477877 8876 454455444
No 53
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.24 E-value=0.17 Score=53.92 Aligned_cols=49 Identities=24% Similarity=0.595 Sum_probs=36.8
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
...+.|.||+..+. ++++++|||.||..|+..-+. ..-.||. |...+..
T Consensus 82 ~sef~c~vc~~~l~--~pv~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY--PPVVTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC--CCccccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 35799999998864 678889999999999766222 2346887 8876653
No 54
>PRK00420 hypothetical protein; Validated
Probab=91.57 E-value=1.3 Score=38.79 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=20.5
Q ss_pred CcCCCCCCcceeecCCCCceEeccccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 310 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~ 310 (548)
...||.|+.|+-+. +=|..||-.|+..
T Consensus 23 ~~~CP~Cg~pLf~l--------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL--------KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec--------CCCceECCCCCCe
Confidence 48999999997751 3356788888876
No 55
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=91.25 E-value=0.33 Score=57.79 Aligned_cols=66 Identities=24% Similarity=0.506 Sum_probs=53.5
Q ss_pred ccccccccccc-ccccCceecCCCCccchhhHHHHHHhhhccCC--ccceecCccccccccchHHHHHhhc
Q 008947 115 STVMCDICMEE-VAGDKATKMDCGHCFCNDCWTEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVS 182 (548)
Q Consensus 115 ~~~~C~IC~e~-~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~--~~~i~CP~~~C~~~i~~~~i~~ll~ 182 (548)
..-.|.|||.+ +.....+.|.|+|.|...|-+..++.+-.... +.-|.||. |...+....++.++.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLld 3553 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLD 3553 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHH
Confidence 44679999988 55556788999999999999999988765543 24579999 999998888888886
No 56
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.15 E-value=0.068 Score=50.51 Aligned_cols=32 Identities=28% Similarity=0.816 Sum_probs=26.7
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHH
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEH 148 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 148 (548)
-.|.|.||-.++. .++...|||.||..|...-
T Consensus 195 IPF~C~iCKkdy~--spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 195 IPFLCGICKKDYE--SPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred Cceeehhchhhcc--chhhhhcchhHHHHHHHHH
Confidence 3589999999984 6778899999999997553
No 57
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.08 E-value=0.88 Score=47.80 Aligned_cols=126 Identities=15% Similarity=0.213 Sum_probs=70.2
Q ss_pred eeeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhh-hCC-------cccCCCCCCC
Q 008947 40 KVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNE-AGV-------TVIDDADPML 111 (548)
Q Consensus 40 ~vlt~~~l~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~-~gl-------~~~~~~~~~~ 111 (548)
..|++......-++-+++-..+||++.....-++...+-..=-.+-.|. .++.. .|. +++-.-....
T Consensus 255 ~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~v~v~aG~~Alp~Llk~~-----~v~~~~~~~W~~~deLPveIeL~~~~ 329 (394)
T KOG2817|consen 255 EILSPKLWKELTEEFTREYCALLGISVESPLSVLVNAGCIALPQLLKYK-----SVMELKHGEWNTKDELPVEIELGKEY 329 (394)
T ss_pred HHhCHHHHHHHHHHHHHHHHHHcCCCccCcHHHHHHhhHHHHHHHHHHH-----HHHHHhccCccccccCccceeccccc
Confidence 3455566666677777888888888876555544433322222222221 11111 111 1100000011
Q ss_pred Ccccccccccccccccc-cCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 112 PLSSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 112 ~~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
..-+.|.|||=-+.-+. +.|..|.|||..|++=+..... +|. ..++||- |+.....+..
T Consensus 330 ~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~-~sfKCPY--CP~e~~~~~~ 389 (394)
T KOG2817|consen 330 HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGS-QSFKCPY--CPVEQLASDT 389 (394)
T ss_pred cccceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCC-eeeeCCC--CCcccCHHhc
Confidence 12356999997776443 4567889999999988776644 343 4799998 8875544433
No 58
>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=90.81 E-value=7.4 Score=40.13 Aligned_cols=53 Identities=28% Similarity=0.670 Sum_probs=34.3
Q ss_pred cCCCCCCCCceEEeccCceeeeeccCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceee
Q 008947 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEK 288 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEK 288 (548)
-|| .|..-....+.-...+. +|||.||..|.... | ..+..+||.|+.++-|
T Consensus 5 ~CP---~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----------~--------------~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCP---RCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----------F--------------VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCC---cCCCCCccCcccccccC-CCCCcccHHHHHHH-----------h--------------cCCCCCCCCCCCccch
Confidence 487 68765444444333455 79999999996431 1 1123589999999886
Q ss_pred cC
Q 008947 289 NG 290 (548)
Q Consensus 289 n~ 290 (548)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 53
No 59
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.73 E-value=0.16 Score=53.10 Aligned_cols=55 Identities=25% Similarity=0.494 Sum_probs=36.8
Q ss_pred cccccccccccccccccC-----cee-cCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 113 LSSTVMCDICMEEVAGDK-----ATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
.+...+|.||++...... ... .+|.|.||..|++.|=...-. +....-.||. |..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv 218 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRV 218 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccC
Confidence 356789999999864322 222 379999999999998643221 2223457998 775
No 60
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.54 E-value=0.048 Score=56.01 Aligned_cols=47 Identities=28% Similarity=0.626 Sum_probs=34.8
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
..+.|+||++-+. .-+....|+|+||.+|+-.-+.. .| =.||. |...
T Consensus 42 ~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~---gn----~ecpt--cRk~ 88 (381)
T KOG0311|consen 42 IQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS---GN----NECPT--CRKK 88 (381)
T ss_pred hhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh---cC----CCCch--HHhh
Confidence 5689999999875 34566699999999998765543 22 36887 6653
No 61
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=90.42 E-value=0.73 Score=47.14 Aligned_cols=79 Identities=16% Similarity=0.305 Sum_probs=48.2
Q ss_pred HHHHHHhcCchhhhhhhCCcccCCCCC--------CCCcccccccccccccccccCceec-CCCCccchhhHHHHHHhhh
Q 008947 83 LLAVLVENGKESLFNEAGVTVIDDADP--------MLPLSSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKI 153 (548)
Q Consensus 83 l~~~~~~~~~~~~~~~~gl~~~~~~~~--------~~~~~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i 153 (548)
+++-|+.++.++.. +.++.++.++++ .........|+||..... ++..+ --|-.||-.|+-.|+..
T Consensus 260 fldWWyssd~~~~~-k~~l~~p~PpPPh~~~~se~e~l~~~~~~CpvClk~r~--Nptvl~vSGyVfCY~Ci~~Yv~~-- 334 (357)
T KOG0826|consen 260 FLDWWYSSDNQRKI-KSTLDPPIPPPPHKQYNSESELLPPDREVCPVCLKKRQ--NPTVLEVSGYVFCYPCIFSYVVN-- 334 (357)
T ss_pred HHHHHhcchHHHhh-ccCCCCCCCcCChhhcccccccCCCccccChhHHhccC--CCceEEecceEEeHHHHHHHHHh--
Confidence 45557754433333 335544433322 112235578999998753 33333 45999999999999983
Q ss_pred ccCCccceecCcccccccc
Q 008947 154 NEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 154 ~~g~~~~i~CP~~~C~~~i 172 (548)
.| +||..+|+..+
T Consensus 335 -~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 335 -YG-----HCPVTGYPASV 347 (357)
T ss_pred -cC-----CCCccCCcchH
Confidence 33 59988887654
No 62
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=89.42 E-value=0.21 Score=51.13 Aligned_cols=47 Identities=23% Similarity=0.628 Sum_probs=35.3
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
...+|.+|-.-+- +......|-|.||+.||-.|+.. .-.||. |...+
T Consensus 14 ~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVI 60 (331)
T ss_pred cceehhhccceee-cchhHHHHHHHHHHHHHHHHHHH--------hccCCc--cceec
Confidence 4589999987653 23344489999999999999987 247998 66544
No 63
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.26 E-value=0.21 Score=51.20 Aligned_cols=52 Identities=31% Similarity=0.615 Sum_probs=37.8
Q ss_pred CCcccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 111 LPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 111 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
.|.++...|+||+-.- ...+..+|+|.-|.+|+.+|+... -+|.. |+..+..
T Consensus 417 lp~sEd~lCpICyA~p--i~Avf~PC~H~SC~~CI~qHlmN~--------k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAGP--INAVFAPCSHRSCYGCITQHLMNC--------KRCFF--CKTTVID 468 (489)
T ss_pred CCCcccccCcceeccc--chhhccCCCCchHHHHHHHHHhcC--------CeeeE--ecceeee
Confidence 3456678999999752 234556999999999999998642 25766 7776543
No 64
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.74 E-value=0.28 Score=51.41 Aligned_cols=49 Identities=22% Similarity=0.672 Sum_probs=37.3
Q ss_pred ccccccccccccc---cCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 116 TVMCDICMEEVAG---DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 116 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
..+||||++.+.. ..++++.|||.|=.+|++.|+. ++ ...+||. |...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~-----~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK-----TKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh-----hhhhCcc--cCChh
Confidence 3689999998542 2467889999999999999993 22 3468998 76543
No 65
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.46 E-value=0.22 Score=55.65 Aligned_cols=45 Identities=29% Similarity=0.786 Sum_probs=35.9
Q ss_pred cccccccccccccc---CceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 116 TVMCDICMEEVAGD---KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 116 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
...|.||.+..... .+..++|+|.||..|++.|++. .-.||. |..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~--CR~ 338 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPT--CRT 338 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCc--chh
Confidence 57899999996421 1678899999999999999987 237998 554
No 66
>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=88.42 E-value=0.11 Score=50.44 Aligned_cols=49 Identities=20% Similarity=0.532 Sum_probs=36.5
Q ss_pred cccccccccc-cccCceec---CCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 117 VMCDICMEEV-AGDKATKM---DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 117 ~~C~IC~e~~-~~~~~~~l---~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
-.||||-.+. -..++..+ .|-|+.|.+|.-..|+. .|-.||-++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence 4799998872 22233333 49999999999988875 35789999998765
No 67
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=87.44 E-value=0.46 Score=39.32 Aligned_cols=31 Identities=19% Similarity=0.482 Sum_probs=24.7
Q ss_pred CCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 135 DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 135 ~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
.|+|.|...|+..++.++-.+ -.||. |...+
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~~-----~~CPm--CR~~w 81 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSSK-----GQCPM--CRQPW 81 (85)
T ss_pred cCccHHHHHHHHHHHccccCC-----CCCCC--cCCee
Confidence 799999999999999985222 37998 87654
No 68
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.34 E-value=0.28 Score=30.34 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=8.4
Q ss_pred CCCCCCcceeec
Q 008947 278 PCPKCHKPVEKN 289 (548)
Q Consensus 278 ~CPkC~~~IEKn 289 (548)
.||+|+..|+.+
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 378888887743
No 69
>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=86.11 E-value=0.57 Score=34.70 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=31.1
Q ss_pred ccccccccccccCceecCCC-----CccchhhHHHHHHhhhccCCccceecCc
Q 008947 118 MCDICMEEVAGDKATKMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
.|-||++.....++...||. |.+...|+..|+..+-+ .+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~------~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGN------KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCC------CcCCC
Confidence 48899984444566677885 88999999999987432 37776
No 70
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.03 E-value=0.38 Score=47.77 Aligned_cols=53 Identities=28% Similarity=0.617 Sum_probs=40.0
Q ss_pred ccccccccccccccc--------CceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 115 STVMCDICMEEVAGD--------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
+...|.||...+..+ +...|+|+|.|...|++.|... | ..-.||- |+..++..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----G--KkqtCPY--CKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----G--KKQTCPY--CKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----c--CCCCCch--HHHHhhHh
Confidence 456799998775422 5688999999999999999765 2 2347998 98877543
No 71
>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=84.71 E-value=0.38 Score=43.20 Aligned_cols=34 Identities=32% Similarity=0.703 Sum_probs=27.6
Q ss_pred ccccccccccccc-cCceecCCC------CccchhhHHHHH
Q 008947 116 TVMCDICMEEVAG-DKATKMDCG------HCFCNDCWTEHF 149 (548)
Q Consensus 116 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~yl 149 (548)
..+|.||++.+.. .-++.+.|| |.||.+|++.|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 5799999999865 345666776 789999999994
No 72
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=84.45 E-value=0.45 Score=49.69 Aligned_cols=45 Identities=31% Similarity=0.752 Sum_probs=33.3
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 169 (548)
.-|-||-+.- .++..-+|||..|..|+..|=.. .+|+ .||.+.|.
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcE 414 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCE 414 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhccc--CCCC----CCCceeeE
Confidence 4699998863 35555699999999999998543 2355 79996665
No 73
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.11 E-value=0.62 Score=50.82 Aligned_cols=37 Identities=35% Similarity=0.755 Sum_probs=31.7
Q ss_pred CcCCC--CCCcceee-cCCCCceEeccccccccccccccc
Q 008947 276 TKPCP--KCHKPVEK-NGGCNLVSCICGQAFCWLCGGATG 312 (548)
Q Consensus 276 tK~CP--kC~~~IEK-n~GCnhMtC~C~~~FCw~C~~~~~ 312 (548)
.|-|| .|+..+.- .+.+.-+.|.||+.|||.|+.+||
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH 197 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence 46676 59998887 888999999999999999998864
No 74
>PHA00626 hypothetical protein
Probab=84.00 E-value=0.75 Score=34.73 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=21.6
Q ss_pred CCCCCCc-ceeecCCCCc----eEe-ccccccccc
Q 008947 278 PCPKCHK-PVEKNGGCNL----VSC-ICGQAFCWL 306 (548)
Q Consensus 278 ~CPkC~~-~IEKn~GCnh----MtC-~C~~~FCw~ 306 (548)
.||+|+. .|-|++-|+. ..| .||+.|=-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 6999998 5888877655 678 488877543
No 75
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.93 E-value=0.81 Score=33.91 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=19.7
Q ss_pred cCCCCCCcceeecC--CCCceEec-ccccc
Q 008947 277 KPCPKCHKPVEKNG--GCNLVSCI-CGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEKn~--GCnhMtC~-C~~~F 303 (548)
+.||.|+.++.... +-+++.|+ ||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46999998887543 35688994 99753
No 76
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.92 E-value=0.95 Score=46.96 Aligned_cols=48 Identities=23% Similarity=0.538 Sum_probs=36.2
Q ss_pred ccccccccccccccccCceecCCCCc-cchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
....+|.||+.+. .+...|+|.|. .|.+|-+..- ... =.||. |...+.
T Consensus 288 ~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPIE 336 (349)
T ss_pred cCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH---Hhh-----cCCCc--cccchH
Confidence 4467999999984 47788999996 8999987764 112 25998 887653
No 77
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=83.67 E-value=0.69 Score=52.56 Aligned_cols=25 Identities=48% Similarity=1.034 Sum_probs=16.4
Q ss_pred cCCCCCCcceeecCCCCceEeccccccccccccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~~ 312 (548)
+.||+|+..+.. +..||..||.+.+
T Consensus 28 ~~Cp~CG~~~~~-----------~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTEVPV-----------DEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCCCCc-----------ccccccccCCccc
Confidence 467777777652 2358888887643
No 78
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.32 E-value=0.5 Score=50.65 Aligned_cols=51 Identities=22% Similarity=0.414 Sum_probs=36.4
Q ss_pred cccccccccccccccc-----Cc----------eecCCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 114 SSTVMCDICMEEVAGD-----KA----------TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~-----~~----------~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
..+..|+||+.+++.. .+ ...+|.|.|...|+.+|..+ ..+.||. |..+++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCC
Confidence 3567899999987521 11 12399999999999999875 2367998 555444
No 79
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=83.18 E-value=4.1 Score=27.98 Aligned_cols=34 Identities=24% Similarity=0.382 Sum_probs=28.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHH
Q 008947 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAV 86 (548)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~ 86 (548)
.+.|.+++++ |.+...|+.-|+..+||++..++.
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 3567888888 999999999999999999987653
No 80
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=82.97 E-value=0.37 Score=47.38 Aligned_cols=47 Identities=23% Similarity=0.481 Sum_probs=33.2
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
+.|..|+---+....+.+.|+|.||..|.+.-. +-.||. |+..+...
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~----------~~~C~l--Ckk~ir~i 50 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS----------PDVCPL--CKKSIRII 50 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC----------cccccc--ccceeeee
Confidence 579988876554455566999999999976422 227988 88765433
No 81
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=82.10 E-value=3.3 Score=36.70 Aligned_cols=109 Identities=16% Similarity=0.265 Sum_probs=52.7
Q ss_pred cchHHHHHhhcc-CChhHHHHHHHHHHHHhhh-cCcccccCCCCCCCCceEEeccCceeeeeccCCCccccCcCccC--C
Q 008947 172 CDEAVVRNLVSK-KHPNLAEKFERFLLESFIE-DNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEA--H 247 (548)
Q Consensus 172 i~~~~i~~ll~~-~~~e~~~ky~~~l~~~~v~-~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~--H 247 (548)
++-...+++++. +|.+-+.+|...+-.+ |. +++-+. | -=...+...+.....+.|.||++||-. ...| |
T Consensus 17 l~w~qt~r~msa~kdhdrf~kylavlqdr-v~~~dpill--p---vg~hlfi~qs~~~rv~rcecghsf~d~-r~nwkl~ 89 (165)
T COG4647 17 LPWPQTRRMMSAYKDHDRFFKYLAVLQDR-VDWDDPILL--P---VGDHLFICQSAQKRVIRCECGHSFGDY-RENWKLH 89 (165)
T ss_pred CCcHHHHHHHhccccHHHHHHHHHHHHhh-cccCCCeee--e---cCCcEEEEecccccEEEEeccccccCh-hhCceee
Confidence 344456666663 3345555555444332 22 222111 2 223333334444446899999999975 3333 2
Q ss_pred CCCCchh-hHHHHHh-hhchHHHHHHHHhCCcCCCCCCccee
Q 008947 248 SPCSCSM-WDLWAKK-CRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 248 ~p~~C~~-~~~w~~~-~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
...--.. ..+.... -..+....+|+...--.||.|+...+
T Consensus 90 a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 90 ANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred eEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 2211100 0011110 01122334677666678999999887
No 82
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.00 E-value=0.84 Score=51.54 Aligned_cols=17 Identities=12% Similarity=0.071 Sum_probs=8.5
Q ss_pred CCCccchhhHHHHHHhh
Q 008947 136 CGHCFCNDCWTEHFIVK 152 (548)
Q Consensus 136 CgH~fC~~C~~~yl~~~ 152 (548)
|+|.+|..||..+...-
T Consensus 121 ~~~~~CP~Ci~s~~DqL 137 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQL 137 (1134)
T ss_pred hhhhhhhHHHHHHHHHh
Confidence 55555555555554443
No 83
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=81.67 E-value=0.61 Score=53.29 Aligned_cols=47 Identities=30% Similarity=0.660 Sum_probs=36.0
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
+.|.||.+ .+.++...|+|.||.+||..++...-. -.||. |...+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC------CCCcH--HHHHHHH
Confidence 79999999 356778899999999999999876322 26766 7665443
No 84
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=81.41 E-value=1 Score=32.30 Aligned_cols=30 Identities=33% Similarity=0.604 Sum_probs=23.1
Q ss_pred HHHHhCCcCCCCCCcceeecCCCCceEec---ccccc
Q 008947 270 NWITVHTKPCPKCHKPVEKNGGCNLVSCI---CGQAF 303 (548)
Q Consensus 270 ~~i~~~tK~CPkC~~~IEKn~GCnhMtC~---C~~~F 303 (548)
.|.....+.||+|++.- |+--+.|+ |++.|
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchhh
Confidence 46667789999999875 77778883 87665
No 85
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.29 E-value=0.82 Score=29.09 Aligned_cols=13 Identities=23% Similarity=0.802 Sum_probs=9.0
Q ss_pred cCCCCCCcceeec
Q 008947 277 KPCPKCHKPVEKN 289 (548)
Q Consensus 277 K~CPkC~~~IEKn 289 (548)
+.||+|+..|+..
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 5788888876543
No 86
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.55 E-value=0.81 Score=44.74 Aligned_cols=47 Identities=30% Similarity=0.765 Sum_probs=29.1
Q ss_pred CCCceEEeccCceeeeeccCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCccee
Q 008947 215 HCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
+|+..+. ....+.|+| ||+.|||-|... |.. +..+.+.||-|+..|.
T Consensus 49 dCNICLd--~akdPVvTl-CGHLFCWpClyq------------Wl~-----------~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 49 DCNICLD--LAKDPVVTL-CGHLFCWPCLYQ------------WLQ-----------TRPNSKECPVCKAEVS 95 (230)
T ss_pred eeeeecc--ccCCCEEee-cccceehHHHHH------------HHh-----------hcCCCeeCCccccccc
Confidence 4544333 223334544 999999999753 332 1235589999998776
No 87
>PLN03086 PRLI-interacting factor K; Provisional
Probab=80.29 E-value=3.7 Score=45.84 Aligned_cols=57 Identities=26% Similarity=0.570 Sum_probs=35.4
Q ss_pred cceecCccccccccchHHHHHhhccCChhHHHHHHHHHHHHhhhcCcccccCCCCCCCCceEEeccCceeeeecc-CCCc
Q 008947 159 KRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (548)
Q Consensus 159 ~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (548)
..+.||. |...++...+...+. .-....+-|| ..+|+..+....... ...|+ |+..
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~-------------------~C~r~~V~Cp-~~~Cg~v~~r~el~~-H~~C~~Cgk~ 462 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEA-------------------YCSRHNVVCP-HDGCGIVLRVEEAKN-HVHCEKCGQA 462 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHh-------------------hCCCcceeCC-cccccceeecccccc-CccCCCCCCc
Confidence 3578998 998887665553332 1223456799 357999887554322 25676 7766
Q ss_pred c
Q 008947 238 F 238 (548)
Q Consensus 238 f 238 (548)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 5
No 88
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.37 E-value=0.86 Score=39.77 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=25.6
Q ss_pred ccCCCCCCCCceEEecc-------Cceeeeecc-CCCccccCcCccCCC
Q 008947 208 KWCPSTPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (548)
+.|- +|+..+.... .......|+ |+..||..|..-+|+
T Consensus 56 ~~C~---~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF---GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc---CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4575 6877654221 112346797 999999999887775
No 89
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=78.41 E-value=0.39 Score=48.31 Aligned_cols=35 Identities=31% Similarity=0.623 Sum_probs=26.5
Q ss_pred HHhCCcCCCCCCcceeecCCCCceEe-ccccccccccccccc
Q 008947 272 ITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATG 312 (548)
Q Consensus 272 i~~~tK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~ 312 (548)
+..++.+|--|-...+ |-+| .|||-|||-|...|-
T Consensus 235 i~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHH
Confidence 4456677777776654 4678 599999999999864
No 90
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.92 E-value=0.7 Score=34.70 Aligned_cols=45 Identities=27% Similarity=0.475 Sum_probs=32.0
Q ss_pred cccccccccccccCceecCCCCc-cchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
-+|.||++.- .+.+.-.|||. .|.+|-...+.. .. -.||. |..++
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~--~~-----g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA--LH-----GCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc--cC-----CcCcc--hhhHH
Confidence 6899999862 23444589996 899998887765 22 25887 77654
No 91
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=77.91 E-value=1.2 Score=33.20 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=19.9
Q ss_pred hCCcCCCCCCc-ceeecCCCCceEe-cccccc
Q 008947 274 VHTKPCPKCHK-PVEKNGGCNLVSC-ICGQAF 303 (548)
Q Consensus 274 ~~tK~CPkC~~-~IEKn~GCnhMtC-~C~~~F 303 (548)
...+.||+|+. .+.... +.++| +||+.+
T Consensus 18 ~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred EccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 34579999998 444333 68999 699865
No 92
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.36 E-value=0.86 Score=47.59 Aligned_cols=47 Identities=28% Similarity=0.670 Sum_probs=33.5
Q ss_pred ccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 117 VMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 117 ~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
..|.||-+-+|.. +...+ .|||.|...|+.+|+...-.. -.||. |..
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~i 53 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQI 53 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eee
Confidence 5799996656543 34455 499999999999999875432 25777 553
No 93
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=76.70 E-value=9.5 Score=26.96 Aligned_cols=38 Identities=24% Similarity=0.344 Sum_probs=32.8
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 008947 52 KEDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (548)
Q Consensus 52 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~~~~~~ 89 (548)
.+.|..+++++ +++.+..+..|..++++++..++.+.+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 35788899999 799999999999999999999998874
No 94
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=76.43 E-value=6.8 Score=39.78 Aligned_cols=37 Identities=22% Similarity=0.385 Sum_probs=30.0
Q ss_pred cccccccccccccC-ceecCCCCccchhhHHHHHHhhh
Q 008947 117 VMCDICMEEVAGDK-ATKMDCGHCFCNDCWTEHFIVKI 153 (548)
Q Consensus 117 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yl~~~i 153 (548)
..|.||+--|...+ +...+|.|+|..-|+..|+....
T Consensus 116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 57888888776555 55669999999999999998744
No 95
>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=76.00 E-value=2.9 Score=42.21 Aligned_cols=48 Identities=25% Similarity=0.652 Sum_probs=33.4
Q ss_pred cccccccc-ccccCceec--CCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 118 MCDICMEE-VAGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 118 ~C~IC~e~-~~~~~~~~l--~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
.||+|-.+ +-..+++.+ +|+|..|.+|+-..+.. .+-.||. |..++.-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cpe--C~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCPE--CMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCCc--ccchhhh
Confidence 48999877 222233333 99999999999988764 2356994 9876643
No 96
>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=75.72 E-value=3.2 Score=27.63 Aligned_cols=28 Identities=25% Similarity=0.655 Sum_probs=16.4
Q ss_pred CCcCCCCCCcceeecCCCCceEe-ccccc
Q 008947 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCnhMtC-~C~~~ 302 (548)
+.+-||+|+.+.....|=--|.| .|++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 34788899888888777677888 48764
No 97
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=75.01 E-value=1.4 Score=47.34 Aligned_cols=37 Identities=32% Similarity=0.835 Sum_probs=30.2
Q ss_pred cccccccccccccccccCcee-cCCCCccchhhHHHHHHh
Q 008947 113 LSSTVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~ 151 (548)
......|++|...+. +++. ..|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc
Confidence 345689999999875 4555 699999999999998775
No 98
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.80 E-value=0.99 Score=45.60 Aligned_cols=44 Identities=27% Similarity=0.711 Sum_probs=33.5
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
.|-|.||-..+- .++...|+|+||..|....+.. | -+|+. |...
T Consensus 241 Pf~c~icr~~f~--~pVvt~c~h~fc~~ca~~~~qk----~----~~c~v--C~~~ 284 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVVTKCGHYFCEVCALKPYQK----G----EKCYV--CSQQ 284 (313)
T ss_pred Cccccccccccc--cchhhcCCceeehhhhcccccc----C----Cccee--cccc
Confidence 467999999873 7788899999999997766542 2 36766 7654
No 99
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=73.72 E-value=2.2 Score=33.37 Aligned_cols=34 Identities=26% Similarity=0.715 Sum_probs=13.9
Q ss_pred cCCCCCCcceee---cCCCCceEec-cccc----cccccccc
Q 008947 277 KPCPKCHKPVEK---NGGCNLVSCI-CGQA----FCWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~IEK---n~GCnhMtC~-C~~~----FCw~C~~~ 310 (548)
-+|++|...+.. .+||.|++|. |=.. -|-+|-.+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTP 49 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCCh
Confidence 589999987765 3788887773 4322 26666554
No 100
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.04 E-value=3.1 Score=28.80 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=21.2
Q ss_pred ccCCCCCCCCceEEeccC----ceeeeecc-CCCcc
Q 008947 208 KWCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-Cg~~f 238 (548)
..|| +|+..+.+.++ ....|.|+ |++.|
T Consensus 3 i~CP---~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP---NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC---CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4688 79999887662 34578998 98876
No 101
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.15 E-value=3.4 Score=28.47 Aligned_cols=28 Identities=29% Similarity=0.797 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEEecc----Cceeeeecc-CCCcc
Q 008947 208 KWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQF 238 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-Cg~~f 238 (548)
..|| +|+..+.+++ .....+.|+ |++.|
T Consensus 3 i~Cp---~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP---NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC---CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4688 7999888765 344578998 98875
No 102
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=72.08 E-value=1.3 Score=45.22 Aligned_cols=84 Identities=26% Similarity=0.606 Sum_probs=46.0
Q ss_pred CccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhccCChhHHHHHHHHH-HHHhhhc----CcccccCCC
Q 008947 138 HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIED----NKMVKWCPS 212 (548)
Q Consensus 138 H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l-~~~~v~~----~~~~~~CP~ 212 (548)
-+||..|-..+.. .|+.||. |...+ +++ +.+...|.-+. ++.|.+. ..+...|-
T Consensus 276 Gy~CP~CkakvCs--------LP~eCpi--C~ltL-------Vss---~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf- 334 (378)
T KOG2807|consen 276 GYFCPQCKAKVCS--------LPIECPI--CSLTL-------VSS---PHLARSYHHLFPLKPFVEIPETEYNGSRFCF- 334 (378)
T ss_pred ceeCCcccCeeec--------CCccCCc--cceeE-------ecc---hHHHHHHHhhcCCcchhhccccccCCCccee-
Confidence 4577777555433 5778887 76543 112 44444454332 2233322 22334564
Q ss_pred CCCCCceEEeccCceeeeecc-CCCccccCcCccCCC
Q 008947 213 TPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHS 248 (548)
Q Consensus 213 ~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (548)
.|+. +........|. |...||..|..-.|.
T Consensus 335 --~C~~----~~~~~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 335 --ACQG----ELLSSGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred --eecc----ccCCCCcEEchhccceeeccchHHHHh
Confidence 4622 12233457997 999999999876564
No 103
>PF04641 Rtf2: Rtf2 RING-finger
Probab=71.49 E-value=3.1 Score=42.06 Aligned_cols=58 Identities=21% Similarity=0.407 Sum_probs=41.5
Q ss_pred cccccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhc
Q 008947 114 SSTVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 182 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~ 182 (548)
...+.|||...++... .++.+ +|||.|+..++++.= .+ -.||. |...+....|-.|-+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNP 170 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecC
Confidence 4679999999998543 34444 999999999999871 11 24998 998877665544443
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=71.10 E-value=1.6 Score=37.27 Aligned_cols=31 Identities=19% Similarity=0.582 Sum_probs=25.4
Q ss_pred ccccccccccccccCceecCCCCccchhhHH
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWT 146 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 146 (548)
...|++|...+....+...||||.|...|.+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4569999999876566666999999999975
No 105
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.09 E-value=3.6 Score=29.82 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=18.3
Q ss_pred cCCCCCCcceeecCCCCceEec-cccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAFC 304 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~~FC 304 (548)
-.||+|+..++-..+=..++|. ||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 4688888888754433367774 776554
No 106
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=69.88 E-value=15 Score=25.00 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=27.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHH
Q 008947 54 DLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLV 88 (548)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~ 88 (548)
.|.++++ +|.+.+.++..|...+||+++..+.++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4555555 599999999999999999999877654
No 107
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.56 E-value=3.2 Score=47.29 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=9.7
Q ss_pred CcCCCCCCccee
Q 008947 276 TKPCPKCHKPVE 287 (548)
Q Consensus 276 tK~CPkC~~~IE 287 (548)
.+.||+|+..+-
T Consensus 41 ~~fC~~CG~~~~ 52 (645)
T PRK14559 41 EAHCPNCGAETG 52 (645)
T ss_pred cccccccCCccc
Confidence 488999988876
No 108
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=69.41 E-value=2 Score=30.67 Aligned_cols=28 Identities=36% Similarity=0.778 Sum_probs=19.5
Q ss_pred CCCCCcceeecCCCCceEecccccccccccccc
Q 008947 279 CPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (548)
Q Consensus 279 CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~ 311 (548)
||-|...+.+ -++=.|||.||..|+..+
T Consensus 1 CpiC~~~~~~-----Pv~l~CGH~FC~~Cl~~~ 28 (42)
T PF15227_consen 1 CPICLDLFKD-----PVSLPCGHSFCRSCLERL 28 (42)
T ss_dssp ETTTTSB-SS-----EEE-SSSSEEEHHHHHHH
T ss_pred CCccchhhCC-----ccccCCcCHHHHHHHHHH
Confidence 5666666552 256679999999999885
No 109
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=69.32 E-value=3.2 Score=29.21 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=25.8
Q ss_pred cCCCCCCcc-eeecCCCCceEe-cccccccccccccccCCC
Q 008947 277 KPCPKCHKP-VEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (548)
Q Consensus 277 K~CPkC~~~-IEKn~GCnhMtC-~C~~~FCw~C~~~~~~~H 315 (548)
..|+.|... +. ++| .|+..+|..|....+.+|
T Consensus 4 ~~C~~H~~~~~~-------~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp SB-SSTTTSBEE-------EEETTTTEEEEHHHHHTSTTTS
T ss_pred ccCccCCccceE-------EEecCCCCccCccCCCCCCCCC
Confidence 689999887 77 999 599999999998755544
No 110
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.09 E-value=2.7 Score=41.41 Aligned_cols=53 Identities=8% Similarity=0.221 Sum_probs=37.6
Q ss_pred ccccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 115 STVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
..+.|+||-+.+... ....| +|||.||.+|....|.. ...||. |...+.+..|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccce
Confidence 568899999997643 22334 99999999999998764 235666 6666655443
No 111
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=68.51 E-value=1.9 Score=44.24 Aligned_cols=53 Identities=25% Similarity=0.508 Sum_probs=37.2
Q ss_pred ccccccccccccc--cCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 116 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 116 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
.-.|+.|.++.+. .+++..+||-..|+-||...-.. + .=+||. |....+++-|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~-l------ngrcpa--crr~y~denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN-L------NGRCPA--CRRKYDDENV 68 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhh-c------cCCChH--hhhhccccce
Confidence 3459999998654 45667799999999999764332 2 237998 8876554433
No 112
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=67.86 E-value=14 Score=24.99 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHH
Q 008947 54 DLRRVMELLSLREHHARTLLIHYRWDVEKLLAVL 87 (548)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~ 87 (548)
.|.++.++ |++.+.|+.-|...+||+++..+-+
T Consensus 4 ~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 44455544 9999999999999999999876643
No 113
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.13 E-value=4.3 Score=47.66 Aligned_cols=36 Identities=33% Similarity=0.661 Sum_probs=24.2
Q ss_pred hhcCcccccCCCCCCCCceEEeccCceeeeecc-CCC-----ccccCcCccC
Q 008947 201 IEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGA-----QFCFSCLSEA 246 (548)
Q Consensus 201 v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~-----~fC~~C~~~~ 246 (548)
++.....+.|| .|+... ....|+ ||. .||..|+...
T Consensus 620 ~eVEVg~RfCp---sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 620 IEVEIGRRKCP---SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred eeecccCccCC---CCCCcC-------CcccCCCCCCCCCcceeCccccCcC
Confidence 33444667898 698763 236888 985 4888887653
No 114
>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=66.01 E-value=3.4 Score=28.30 Aligned_cols=27 Identities=37% Similarity=0.943 Sum_probs=17.1
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCc
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (548)
++|| .|++.+.+..+....+.|. |++.
T Consensus 2 ~FCp---~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP---ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BET---TTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCC---CCCccceEcCCCccCcCCCCCCCc
Confidence 5798 7999998766433333675 7664
No 115
>PHA03096 p28-like protein; Provisional
Probab=65.98 E-value=3.4 Score=42.27 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=28.7
Q ss_pred cccccccccccc----cCcee-c-CCCCccchhhHHHHHHhhh
Q 008947 117 VMCDICMEEVAG----DKATK-M-DCGHCFCNDCWTEHFIVKI 153 (548)
Q Consensus 117 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~C~~~yl~~~i 153 (548)
..|+||++.... +..+. | .|.|.||..|++.|..++.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~ 221 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL 221 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh
Confidence 689999998542 22233 3 8999999999999998865
No 116
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.48 E-value=1.7 Score=40.77 Aligned_cols=29 Identities=34% Similarity=0.981 Sum_probs=21.7
Q ss_pred cCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCccee
Q 008947 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
.||+.||..|.+. ...++..||-|++.|.
T Consensus 150 kCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 150 KCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 4999999999653 1234589999998665
No 117
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=65.42 E-value=3.2 Score=41.89 Aligned_cols=43 Identities=26% Similarity=0.776 Sum_probs=32.5
Q ss_pred cccccccccccccCceec-CCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 117 VMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
+.|+.|-..+. ++... .|+|.||..|+..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhh--CcccCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 78999988753 44444 89999999999876654 3478998 764
No 118
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=65.02 E-value=3.8 Score=43.56 Aligned_cols=10 Identities=30% Similarity=1.016 Sum_probs=5.7
Q ss_pred cccccccccc
Q 008947 118 MCDICMEEVA 127 (548)
Q Consensus 118 ~C~IC~e~~~ 127 (548)
.|.-|-.++.
T Consensus 276 iC~~C~K~V~ 285 (468)
T KOG1701|consen 276 ICAFCHKTVS 285 (468)
T ss_pred hhhhcCCccc
Confidence 5666665543
No 119
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=64.89 E-value=2.8 Score=38.30 Aligned_cols=10 Identities=30% Similarity=0.571 Sum_probs=5.1
Q ss_pred cccccccccc
Q 008947 115 STVMCDICME 124 (548)
Q Consensus 115 ~~~~C~IC~e 124 (548)
+..+|||=.+
T Consensus 125 eEg~CPIVIe 134 (167)
T PF05320_consen 125 EEGTCPIVIE 134 (167)
T ss_pred hcCCCcEEEe
Confidence 3455666444
No 120
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=64.28 E-value=5 Score=26.56 Aligned_cols=26 Identities=27% Similarity=0.722 Sum_probs=12.6
Q ss_pred cCCCCCCcceeecCCCCceEe-cccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 303 (548)
-.||+|+....-.+|.+ |.| .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccccC
Confidence 37999998887777754 678 488875
No 121
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=63.86 E-value=26 Score=24.73 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=33.3
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 008947 52 KEDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (548)
Q Consensus 52 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~~~~~~ 89 (548)
.+.+..+++++ +++...++..|..++++++..++.+.+
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 45778888898 799999999999999999999988763
No 122
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=63.61 E-value=10 Score=39.06 Aligned_cols=53 Identities=21% Similarity=0.455 Sum_probs=36.2
Q ss_pred cccccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhh
Q 008947 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLV 181 (548)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll 181 (548)
...-++||||++.+.+ ..+..+=||..|.+|-.. ..-+||. |...++ .++.+.
T Consensus 45 ~~~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g--~~R~~a 97 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG--NIRCRA 97 (299)
T ss_pred chhhccCchhhccCcc-cceecCCCcEehhhhhhh-----------hcccCCc--cccccc--cHHHHH
Confidence 3456899999998742 233334489999999762 2458998 988877 344443
No 123
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=63.32 E-value=4.5 Score=46.47 Aligned_cols=50 Identities=26% Similarity=0.441 Sum_probs=38.1
Q ss_pred cccccccccccccccC-ceec-CCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 115 STVMCDICMEEVAGDK-ATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
..++|.||++.+.... +.+. .|-|.|-..|++.|....-.+|. ...+||.
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~ 241 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA 241 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc
Confidence 4689999999976543 4444 78899999999999988544444 4568886
No 124
>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=63.28 E-value=7.1 Score=26.86 Aligned_cols=28 Identities=32% Similarity=0.814 Sum_probs=19.4
Q ss_pred ccCCCCCCCCceEEeccC----ceeeeecc-CCCcc
Q 008947 208 KWCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-Cg~~f 238 (548)
.-|| +|+..+.+.+. ....+.|+ |++.|
T Consensus 3 ~~CP---~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP---NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC---CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 3587 79998887652 23368897 88764
No 125
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=62.51 E-value=4.9 Score=34.02 Aligned_cols=28 Identities=36% Similarity=0.762 Sum_probs=20.7
Q ss_pred cCCCCCCcce--eecCCCCceEec-cccccc
Q 008947 277 KPCPKCHKPV--EKNGGCNLVSCI-CGQAFC 304 (548)
Q Consensus 277 K~CPkC~~~I--EKn~GCnhMtC~-C~~~FC 304 (548)
..||.|+..+ ++.+-||...|+ |++.|=
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 3699998654 455559999995 998763
No 126
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=62.33 E-value=6.8 Score=26.71 Aligned_cols=31 Identities=19% Similarity=0.428 Sum_probs=24.6
Q ss_pred CCCCCCc-ceeecCCCCceEec-ccccccccccccccCCC
Q 008947 278 PCPKCHK-PVEKNGGCNLVSCI-CGQAFCWLCGGATGRDH 315 (548)
Q Consensus 278 ~CPkC~~-~IEKn~GCnhMtC~-C~~~FCw~C~~~~~~~H 315 (548)
.||.|.. ++. ++|. |+...|..|....+.+|
T Consensus 2 ~C~~H~~~~~~-------~fC~~~~~~iC~~C~~~~H~~H 34 (39)
T cd00021 2 LCDEHGEEPLS-------LFCETDRALLCVDCDLSVHSGH 34 (39)
T ss_pred CCCccCCcceE-------EEeCccChhhhhhcChhhcCCC
Confidence 5888977 888 9994 99999999986534444
No 127
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=62.30 E-value=4.2 Score=47.34 Aligned_cols=26 Identities=42% Similarity=1.136 Sum_probs=22.5
Q ss_pred cCCCCCCcceeecCCCCceEec-cccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAFC 304 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~~FC 304 (548)
..||.|+..+...+|| ++|+ ||+-=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC--~~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGC--VVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCC--CcCCCCCCCCC
Confidence 3699999999999999 5995 998766
No 128
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=61.93 E-value=5.5 Score=29.41 Aligned_cols=26 Identities=27% Similarity=0.604 Sum_probs=14.7
Q ss_pred CcCCCCCCcceeecCCCCceEe-cccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQ 301 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC-~C~~ 301 (548)
-+.||+|+--+--..-=+...| +||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 3789999853332211224667 6775
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.65 E-value=6.3 Score=47.52 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHH-------HHhhhhhhhc
Q 008947 472 QVINLSVITDTLCKKMYEC-------IENDLLGCLQ 500 (548)
Q Consensus 472 ~~~~l~~~~~~~~~~l~~~-------~e~~l~~~~~ 500 (548)
-+...++.+|.+..++|.. =.++|.|-|.
T Consensus 846 yl~~va~fiDdLL~k~Ygl~~fYn~~~~eDLiGhLv 881 (1337)
T PRK14714 846 YLLKVAKFVDDLLEKFYGLPRFYNVEKREDLVGHLV 881 (1337)
T ss_pred HHHHHHHHHHHHHHHhhCCCcccCCCChhhccceee
Confidence 3455677777777776643 2346776665
No 130
>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=59.85 E-value=6.6 Score=31.33 Aligned_cols=32 Identities=41% Similarity=0.970 Sum_probs=21.1
Q ss_pred CCCCCCcceeecCCCCceEe-cccc-----cccccccccc
Q 008947 278 PCPKCHKPVEKNGGCNLVSC-ICGQ-----AFCWLCGGAT 311 (548)
Q Consensus 278 ~CPkC~~~IEKn~GCnhMtC-~C~~-----~FCw~C~~~~ 311 (548)
.||.|+.+++.++ .+.+| .|+. .+|-.|+.+.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 6999999999888 67999 5885 4799998773
No 131
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=59.66 E-value=3.5 Score=39.57 Aligned_cols=32 Identities=31% Similarity=0.746 Sum_probs=23.8
Q ss_pred CcCCCCCCcceeecCCCCceEeccccccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~~ 312 (548)
.-.||-|.-.+..- +.=.|||-|||.|...|-
T Consensus 18 ~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCCc-----EEcCCCchhHHHHHHHHH
Confidence 35899998876421 333699999999998873
No 132
>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=59.46 E-value=6.8 Score=30.76 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=18.8
Q ss_pred CCcCCCCCCcceeecCCCCceEec-cccc
Q 008947 275 HTKPCPKCHKPVEKNGGCNLVSCI-CGQA 302 (548)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCnhMtC~-C~~~ 302 (548)
.++.||.|+....++..=..++|. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 468999999999873333345663 6543
No 133
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=59.14 E-value=3.4 Score=46.97 Aligned_cols=30 Identities=30% Similarity=0.867 Sum_probs=21.6
Q ss_pred cCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCccee
Q 008947 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
.|||.||+.|-.. .+....+.||+|+.+.-
T Consensus 660 kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-------------------------RYETRQRKCPKCNAAFG 689 (698)
T ss_pred hcchHHHHHHHHH-------------------------HHHHhcCCCCCCCCCCC
Confidence 4999999999653 11223489999998764
No 134
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.96 E-value=6.5 Score=38.26 Aligned_cols=54 Identities=20% Similarity=0.413 Sum_probs=41.4
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
-.|..|-.++...+.+.|.|-|.|.-.|+.+.-..--.+..-.-.+||. |...+
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 4699999998888999999999999999998765433322223578998 88644
No 135
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=58.12 E-value=4.2 Score=30.79 Aligned_cols=45 Identities=24% Similarity=0.572 Sum_probs=30.2
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
...|-.|...- .....++|||..|..||-.- .---||. |...+..
T Consensus 7 ~~~~~~~~~~~--~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFVG--TKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEF 51 (55)
T ss_pred ceeEEEccccc--cccccccccceeeccccChh----------hccCCCC--CCCcccC
Confidence 35566665542 34567899999999998642 1235888 8776643
No 136
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.11 E-value=5.7 Score=39.66 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=18.4
Q ss_pred CCCCCCcceeecCCCCceEe-ccccccccccc
Q 008947 278 PCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCG 308 (548)
Q Consensus 278 ~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~ 308 (548)
.|+.+... .+++| .|+...|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEecccccccCCCCC
Confidence 45555544 56999 59999999998
No 137
>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=57.53 E-value=4 Score=30.52 Aligned_cols=35 Identities=20% Similarity=0.562 Sum_probs=17.2
Q ss_pred CCCceEEecc---Cceeeeecc-CCCccccCcCccCCCC
Q 008947 215 HCGNAIRVEE---VEVCEVECA-CGAQFCFSCLSEAHSP 249 (548)
Q Consensus 215 ~C~~~i~~~~---~~~~~v~C~-Cg~~fC~~C~~~~H~p 249 (548)
+|...+.... .......|+ |+..||..|-.-.|+-
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 4655544321 113467998 9999999998777764
No 138
>PF14369 zf-RING_3: zinc-finger
Probab=57.12 E-value=8.5 Score=26.39 Aligned_cols=28 Identities=29% Similarity=0.883 Sum_probs=19.2
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCcc
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQF 238 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~f 238 (548)
-||- .|.+.|.+.......+.|| |+..|
T Consensus 3 ywCh---~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH---QCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCc---cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 3897 7999998754333345687 87655
No 139
>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=56.71 E-value=6.2 Score=34.35 Aligned_cols=25 Identities=32% Similarity=0.909 Sum_probs=16.2
Q ss_pred cCCCCCCcceee-cCCCCceEe-cccccc
Q 008947 277 KPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEK-n~GCnhMtC-~C~~~F 303 (548)
+.||+|++..-- |- +.++| +||..|
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 579999876542 32 56777 476655
No 140
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=56.20 E-value=4.2 Score=42.63 Aligned_cols=48 Identities=23% Similarity=0.643 Sum_probs=37.0
Q ss_pred ccccccccccccc--ccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 115 STVMCDICMEEVA--GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 115 ~~~~C~IC~e~~~--~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
....|..|-+.+. .+....|+|.|.|...|+..|+.. ++ +-.||. |..
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HHH
Confidence 4578999999864 345667899999999999999943 33 357988 773
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.53 E-value=8.7 Score=44.37 Aligned_cols=35 Identities=29% Similarity=0.790 Sum_probs=28.9
Q ss_pred CcCCCCCCcceeecCCCCceEec-cccc-----cccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSCI-CGQA-----FCWLCGGA 310 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC~-C~~~-----FCw~C~~~ 310 (548)
+-.||+|..++.-..+=|.|.|. ||++ .|..||+.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 46799999888765555899995 9987 89999987
No 142
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=55.47 E-value=3 Score=42.90 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=21.7
Q ss_pred CcCCCCCCcceee-cCCCCceEe-cccccc
Q 008947 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (548)
Q Consensus 276 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 303 (548)
|..||+|+..|-+ .-.=|.+.| +|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 5899999988864 345567899 599988
No 143
>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=55.17 E-value=10 Score=27.01 Aligned_cols=22 Identities=36% Similarity=1.126 Sum_probs=16.2
Q ss_pred cCCCCCCcceee-cCCCCceEe-ccc
Q 008947 277 KPCPKCHKPVEK-NGGCNLVSC-ICG 300 (548)
Q Consensus 277 K~CPkC~~~IEK-n~GCnhMtC-~C~ 300 (548)
..||.|+.|+-+ ..| .++| .|+
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 689999999987 445 4666 353
No 144
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=54.47 E-value=3.1e+02 Score=32.01 Aligned_cols=48 Identities=13% Similarity=0.240 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHH
Q 008947 432 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVIT 480 (548)
Q Consensus 432 ~~~lfe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~ 480 (548)
+.+-..+.|+.|.+.++.|...+.......+..| ++++.++..+..-+
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AE-r~~~~EL~~~~~~l 648 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAE-REFKKELERMKDQL 648 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHH-HHHHHHHHHHHHHH
Confidence 4556777899999999999988876555444433 34444444444433
No 145
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.45 E-value=14 Score=37.28 Aligned_cols=54 Identities=24% Similarity=0.527 Sum_probs=39.4
Q ss_pred ccccccccccccccccCceecC--CCCccchhhHHHHHHhhhccCCccceecCc-ccccc
Q 008947 114 SSTVMCDICMEEVAGDKATKMD--CGHCFCNDCWTEHFIVKINEGQSKRIRCMA-HKCNA 170 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~-~~C~~ 170 (548)
+..+.|.+|-|-+....++..+ =.|.||.-|-++.|+.+-..| .+.||. .+|..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg---evYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG---EVYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC---ceeCCCCCcCcc
Confidence 4568999999987644444332 269999999999999866555 488986 46764
No 146
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=54.16 E-value=6.2 Score=32.02 Aligned_cols=54 Identities=22% Similarity=0.633 Sum_probs=21.0
Q ss_pred CCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCC
Q 008947 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 293 (548)
-|+--|.........|-|. |+...|..|.. +. ++..++.||.|+.+..+..|+-
T Consensus 14 iCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE----------YE---------------rkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 14 ICGDDVGLTENGEVFVACHECAFPVCRPCYE----------YE---------------RKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp SS--B--B-SSSSB--S-SSS-----HHHHH----------HH---------------HHTS-SB-TTT--B----TT--
T ss_pred cccCccccCCCCCEEEEEcccCCccchhHHH----------HH---------------hhcCcccccccCCCcccccCCC
Confidence 6887777666666778997 99998888743 11 2345589999999988777653
No 147
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=53.66 E-value=1.2 Score=36.36 Aligned_cols=48 Identities=33% Similarity=0.413 Sum_probs=34.6
Q ss_pred eCHHHHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHcCCChHHHHHHHHhc
Q 008947 42 ITRESLLAAQKEDLRRVMELLSL---REHHARTLLIHYRWDVEKLLAVLVEN 90 (548)
Q Consensus 42 lt~~~l~~~~~~~i~~v~~~l~i---~~~~a~~LL~~~~W~~~~l~~~~~~~ 90 (548)
||+++- ..+.+-+.+|.++||= +.....--|.+|.|++++-+..+..+
T Consensus 20 Ls~ed~-~~L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 20 LSPEDQ-AQLYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -TCHHH-HHHCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CCHHHH-HHHHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 455553 3477788899999974 55567888899999999998888753
No 148
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=53.38 E-value=3.5 Score=33.28 Aligned_cols=48 Identities=27% Similarity=0.583 Sum_probs=33.0
Q ss_pred ccccccccccc---------cC-ceec-CCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 118 MCDICMEEVAG---------DK-ATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 118 ~C~IC~e~~~~---------~~-~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
+|.||--.|.. ++ +..+ -|.|.|-.-|+..++.+.-++|+ ||. |...+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~-----CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQ-----CPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccccc-----CCc--chhee
Confidence 67777665542 22 1222 68999999999999988766654 888 76543
No 149
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=52.89 E-value=8.5 Score=46.45 Aligned_cols=55 Identities=27% Similarity=0.362 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHh-cccCCCC---CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 008947 441 QQLEANVEKLSKFL-EEPFDQY---PDDKVMEIRMQVINLSVITDTLCKKMYECIENDLL 496 (548)
Q Consensus 441 ~~lE~~~E~L~~~l-e~~~~~~---~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~ 496 (548)
..+--.+|+|.++= ++++... .++.|.++|.+=+-|+.-.-.|+-+.-+.|- +||
T Consensus 800 ~Eigvs~eklreLGY~~Di~G~pL~~~dQivELk~QDiil~~~aa~yl~~va~fiD-dLL 858 (1337)
T PRK14714 800 REIGVSVEKLRELGYTQDIHGDPLVHEDQVVELKVQDIVLSDGAAEYLLKVAKFVD-DLL 858 (1337)
T ss_pred HHcCCCHHHHHHcCCccccCCCCCCCccceEEeecccEEcchHHHHHHHHHHHHHH-HHH
Confidence 34555677777662 3333221 2455777777777777777778877777774 555
No 150
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=52.84 E-value=8.4 Score=34.61 Aligned_cols=24 Identities=46% Similarity=1.148 Sum_probs=18.4
Q ss_pred CcCCCCCCcceeecCCCCceEeccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCG 308 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~ 308 (548)
.+.||.|+.|+.+- -|.-||-+|+
T Consensus 28 ~~hCp~Cg~PLF~K---------dG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRK---------DGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceee---------CCeEECCCCC
Confidence 37999999998753 4467777777
No 151
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=52.67 E-value=5.4 Score=40.66 Aligned_cols=54 Identities=26% Similarity=0.575 Sum_probs=38.4
Q ss_pred cCcccccCCCCCCCCceEEeccCceeeeeccCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCC
Q 008947 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKC 282 (548)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC 282 (548)
.++.+.+|- .|+..|.+=+.- =+|.+.||..|... |+ .|.||.|
T Consensus 86 l~p~VHfCd---~Cd~PI~IYGRm-----IPCkHvFCl~CAr~-~~---------------------------dK~Cp~C 129 (389)
T KOG2932|consen 86 LGPRVHFCD---RCDFPIAIYGRM-----IPCKHVFCLECARS-DS---------------------------DKICPLC 129 (389)
T ss_pred cCcceEeec---ccCCcceeeecc-----cccchhhhhhhhhc-Cc---------------------------cccCcCc
Confidence 345677786 799877643221 15999999999653 21 1899999
Q ss_pred CcceeecCCC
Q 008947 283 HKPVEKNGGC 292 (548)
Q Consensus 283 ~~~IEKn~GC 292 (548)
.-.|+|.+-|
T Consensus 130 ~d~VqrIeq~ 139 (389)
T KOG2932|consen 130 DDRVQRIEQI 139 (389)
T ss_pred ccHHHHHHHh
Confidence 9999987655
No 152
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=52.39 E-value=11 Score=27.67 Aligned_cols=26 Identities=35% Similarity=0.882 Sum_probs=17.0
Q ss_pred cCCCCCCCCceEEeccCce-eeeecc-CCCc
Q 008947 209 WCPSTPHCGNAIRVEEVEV-CEVECA-CGAQ 237 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~~ 237 (548)
+|| .||..+....... ....|+ ||+.
T Consensus 2 FCp---~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP---KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC---CCCCccccccCCCCCEEECCcCCCe
Confidence 688 7999887654322 356776 7754
No 153
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=52.03 E-value=15 Score=26.59 Aligned_cols=28 Identities=32% Similarity=0.901 Sum_probs=20.3
Q ss_pred cCCCCCCCCceEEeccCceeeeecc-CCCcccc
Q 008947 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCF 240 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~ 240 (548)
.|| +|+..+....... .+.|| ||..+=.
T Consensus 5 ~C~---~CG~~~~~~~~~~-~~~Cp~CG~~~~~ 33 (46)
T PRK00398 5 KCA---RCGREVELDEYGT-GVRCPYCGYRILF 33 (46)
T ss_pred ECC---CCCCEEEECCCCC-ceECCCCCCeEEE
Confidence 587 7999888766443 57898 9887544
No 154
>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=50.38 E-value=13 Score=27.77 Aligned_cols=11 Identities=45% Similarity=0.942 Sum_probs=8.6
Q ss_pred cCCCCCCccee
Q 008947 277 KPCPKCHKPVE 287 (548)
Q Consensus 277 K~CPkC~~~IE 287 (548)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 89999986544
No 155
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.25 E-value=13 Score=39.19 Aligned_cols=6 Identities=33% Similarity=0.872 Sum_probs=3.5
Q ss_pred cccccc
Q 008947 121 ICMEEV 126 (548)
Q Consensus 121 IC~e~~ 126 (548)
||++.-
T Consensus 396 Ic~~ts 401 (514)
T KOG3130|consen 396 ICSDTS 401 (514)
T ss_pred ccccCC
Confidence 666553
No 156
>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=50.18 E-value=13 Score=41.31 Aligned_cols=34 Identities=26% Similarity=0.677 Sum_probs=22.6
Q ss_pred cCCCCCCcceeecCCCCceEe-ccccc-----cccccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~ 310 (548)
-.||+|..++.--..=|.+.| .||+. .|-.|++.
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 478888777653223346888 48865 68888775
No 157
>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=49.65 E-value=4 Score=32.57 Aligned_cols=39 Identities=23% Similarity=0.515 Sum_probs=22.2
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
..||.|-.++.... +|.+|..|-..|.. ...||. |...+
T Consensus 2 ~~CP~C~~~L~~~~------~~~~C~~C~~~~~~---------~a~CPd--C~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQG------GHYHCEACQKDYKK---------EAFCPD--CGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEET------TEEEETTT--EEEE---------EEE-TT--T-SB-
T ss_pred CcCCCCCCccEEeC------CEEECcccccccee---------cccCCC--cccHH
Confidence 57999988764322 89999999887643 357988 87654
No 158
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=49.36 E-value=6.9 Score=33.29 Aligned_cols=33 Identities=18% Similarity=0.473 Sum_probs=24.5
Q ss_pred CcccccccccccccccccCceecCCCCccchhh
Q 008947 112 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144 (548)
Q Consensus 112 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 144 (548)
.....|+|.-||-....+....-.=|+.+|++|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 345789999999886555444444589999998
No 159
>PF12773 DZR: Double zinc ribbon
Probab=48.87 E-value=7.7 Score=28.39 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=7.8
Q ss_pred cCCCCCCcceee
Q 008947 277 KPCPKCHKPVEK 288 (548)
Q Consensus 277 K~CPkC~~~IEK 288 (548)
+.||+|+..+..
T Consensus 30 ~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 30 KICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCCcC
Confidence 567777776654
No 160
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=48.64 E-value=8.8 Score=44.72 Aligned_cols=51 Identities=20% Similarity=0.406 Sum_probs=36.3
Q ss_pred cccccccccccccccC---c--eecCCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 115 STVMCDICMEEVAGDK---A--TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~---~--~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
...+|+||+..+...+ | ....|.|.|...|+-.|+.+.- .-+||. |...++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--cccccc
Confidence 4468999999865221 2 1226899999999999998732 247998 876543
No 161
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=48.52 E-value=4.3 Score=41.68 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=14.4
Q ss_pred cCCCCCCcceee-cCCCCceEe-cccccc
Q 008947 277 KPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEK-n~GCnhMtC-~C~~~F 303 (548)
.+||+|+..|-+ .-.=|...| .|+|+|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 566666666543 223344566 366644
No 162
>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=48.41 E-value=12 Score=32.11 Aligned_cols=24 Identities=38% Similarity=0.890 Sum_probs=17.6
Q ss_pred cCCCCCCcceeecCCCCceEe-ccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~~ 302 (548)
+.||+|+.++...+| .+.| .|++.
T Consensus 1 ~fC~~Cg~~l~~~~~--~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKNG--VYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCCC--eEECcCCCCc
Confidence 369999998876543 7888 47775
No 163
>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=48.12 E-value=28 Score=30.66 Aligned_cols=42 Identities=24% Similarity=0.592 Sum_probs=29.1
Q ss_pred CCcCCCCCCcceeecCCCCceEe-cccccccccccccccCCCCc
Q 008947 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTW 317 (548)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~~~H~w 317 (548)
+.+.|..|+.+.-.-++.. ..| .|++.+|-.|+........|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~~~~~~~W 95 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVYSKKEPIW 95 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEETSSSCCE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCcCCCCCCE
Confidence 5689999998866544444 889 49999999999874334444
No 164
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.66 E-value=9.7 Score=44.17 Aligned_cols=39 Identities=28% Similarity=0.637 Sum_probs=31.2
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhh
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKI 153 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i 153 (548)
..-+|.+|.-.+-....+..+|||.|..+|+..++....
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHccc
Confidence 346899999887655566669999999999999876533
No 165
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=47.16 E-value=14 Score=25.14 Aligned_cols=27 Identities=33% Similarity=0.872 Sum_probs=13.6
Q ss_pred ccCCCCCCCCceEEe---ccCceeeeecc-CCCc
Q 008947 208 KWCPSTPHCGNAIRV---EEVEVCEVECA-CGAQ 237 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~---~~~~~~~v~C~-Cg~~ 237 (548)
++|| .|+..+.. .++......|+ ||..
T Consensus 1 kfC~---~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP---QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T---TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc---cccChhhhhcCCCCCccceECCCCCCE
Confidence 4788 79988764 33555667887 8764
No 166
>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=46.17 E-value=5.1 Score=41.04 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=20.1
Q ss_pred CcCCCCCCcceeec-CCCCceEe-cccccc
Q 008947 276 TKPCPKCHKPVEKN-GGCNLVSC-ICGQAF 303 (548)
Q Consensus 276 tK~CPkC~~~IEKn-~GCnhMtC-~C~~~F 303 (548)
|..||+|+..|-+. -.=|.+.| .|+++|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 57899999887653 34456788 588875
No 167
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=46.16 E-value=4.6 Score=29.85 Aligned_cols=34 Identities=29% Similarity=0.773 Sum_probs=27.7
Q ss_pred cccccccccccccccCceec-CCCCccchhhHHHH
Q 008947 115 STVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEH 148 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~y 148 (548)
..++|..|-+.++..+.... -||---|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 46899999999876665544 79999999999874
No 168
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.99 E-value=18 Score=34.07 Aligned_cols=57 Identities=25% Similarity=0.472 Sum_probs=38.4
Q ss_pred ccccccccccc-ccccC----ceecCCCCccchhhHHHHHHhhhccCCccce---ecCccccccccc
Q 008947 115 STVMCDICMEE-VAGDK----ATKMDCGHCFCNDCWTEHFIVKINEGQSKRI---RCMAHKCNAICD 173 (548)
Q Consensus 115 ~~~~C~IC~e~-~~~~~----~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i---~CP~~~C~~~i~ 173 (548)
....|.||+-- +...- .-...||..|..-|+..|+..-+...+++.| .||- |..++.
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 34567777653 11111 1234799999999999999988777776555 5877 776654
No 169
>smart00336 BBOX B-Box-type zinc finger.
Probab=45.80 E-value=19 Score=24.82 Aligned_cols=32 Identities=34% Similarity=0.785 Sum_probs=25.7
Q ss_pred cCCCCCC-cceeecCCCCceEe-cccccccccccccccCCC
Q 008947 277 KPCPKCH-KPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (548)
Q Consensus 277 K~CPkC~-~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~~~H 315 (548)
..|+.|. .++. ++| .|....|..|....+.+|
T Consensus 4 ~~C~~h~~~~~~-------~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred CcCCCCCCCceE-------EECCCCCcccccccChhhcCCC
Confidence 5799998 8888 999 599999999986644444
No 170
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=45.56 E-value=2.9e+02 Score=27.66 Aligned_cols=99 Identities=10% Similarity=0.244 Sum_probs=63.1
Q ss_pred cccchhHHHHHHHHHHHHhHhhhccceeeeeccCccccccccChHHHHHhHHHHHHHHHHHHHHHHHHHHHhcccCCCCC
Q 008947 383 RLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYP 462 (548)
Q Consensus 383 ~~~~~~~l~~a~~~l~~~R~~L~~sy~~~yy~~~~~~~~~~~~~~e~~~~~~lfe~~Q~~lE~~~E~L~~~le~~~~~~~ 462 (548)
+++++-.+..|++.++.-|-.+...|...== ..+ ..+ .-+.-.+..-+.+|..++.-+..|..++.++.
T Consensus 140 ~Lkeyv~y~~slK~vlk~R~~~Q~~le~k~e---------~l~-k~~-~dr~~~~~ev~~~e~kve~a~~~~k~e~~Rf~ 208 (243)
T cd07666 140 VIHEYVLYSETLMGVIKRRDQIQAELDSKVE---------ALA-NKK-ADRDLLKEEIEKLEDKVECANNALKADWERWK 208 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHH-hhh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777888998888877655544322100 000 000 11133444455566666667777777777777
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008947 463 DDKVMEIRMQVINLSVITDTLCKKMYECIE 492 (548)
Q Consensus 463 ~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (548)
.++..++|.-+++.+..--.++++++..-|
T Consensus 209 ~~k~~D~k~~~~~yae~~i~~~~~~~~~We 238 (243)
T cd07666 209 QNMQTDLRSAFTDMAENNISYYEECLATWE 238 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777888888888888888788888877766
No 171
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.49 E-value=15 Score=42.22 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=21.8
Q ss_pred cCCCCCCcceeecCCCCceEec-cccc----cccccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQA----FCWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~~----FCw~C~~~ 310 (548)
-.||+|..++.-..+=+.+.|. ||+. .|-.|++.
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 4677777776644344568884 8763 57777664
No 172
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.30 E-value=9.2 Score=38.75 Aligned_cols=28 Identities=32% Similarity=0.909 Sum_probs=22.7
Q ss_pred ccccccccccccccCceecCCCCc-cchhhH
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCW 145 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~ 145 (548)
..-|.||++.. .+.+.|+|||. -|..|=
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhc
Confidence 57899999973 47899999996 687773
No 173
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=45.27 E-value=16 Score=30.33 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=20.9
Q ss_pred CcCCCCCCcceeecCCCCceEe-cccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 303 (548)
-..||.|+++.-|..+=---.| +||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3689999999888766555667 477766
No 174
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=45.21 E-value=15 Score=39.49 Aligned_cols=19 Identities=32% Similarity=0.522 Sum_probs=11.4
Q ss_pred CCCCccccccccccccccc
Q 008947 109 PMLPLSSTVMCDICMEEVA 127 (548)
Q Consensus 109 ~~~~~~~~~~C~IC~e~~~ 127 (548)
+.+|.+..|.|.-==++-+
T Consensus 187 P~LPDSTDFVCGTLDEDRP 205 (458)
T PF10446_consen 187 PELPDSTDFVCGTLDEDRP 205 (458)
T ss_pred CCCCCcccccCCCcCCcch
Confidence 4556677787775444433
No 175
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=44.24 E-value=6.6 Score=40.03 Aligned_cols=89 Identities=25% Similarity=0.506 Sum_probs=47.4
Q ss_pred CCccchhhHHHHHHhhhccCCccceecCccccccccchHHHHHhhccCChhHHHHHHHHH-HHHhhhcCc----ccccCC
Q 008947 137 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIEDNK----MVKWCP 211 (548)
Q Consensus 137 gH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l-~~~~v~~~~----~~~~CP 211 (548)
|-++|..|-..-. ..||.||. |... -+++ ..+...|..+. ++.+++... .-..|-
T Consensus 307 gGy~CP~CktkVC--------sLPi~CP~--Csl~-------Lils---thLarSyhhL~PLk~f~E~p~~~~~ks~~Cf 366 (421)
T COG5151 307 GGYECPVCKTKVC--------SLPISCPI--CSLQ-------LILS---THLARSYHHLYPLKPFVEKPEGTNPKSTHCF 366 (421)
T ss_pred CceeCCcccceee--------cCCccCcc--hhHH-------HHHH---HHHHHHHHhhccCcccccccCCCCCCCccce
Confidence 4467777743322 25778886 5432 2333 34445554332 344554322 233454
Q ss_pred CCCCCCceEEecc-------Cceeeeecc-CCCccccCcCccCCC
Q 008947 212 STPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (548)
Q Consensus 212 ~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (548)
.|+..+.... .......|. |...||..|..-.|.
T Consensus 367 ---~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 367 ---VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ---eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 4655444222 122356897 999999999765553
No 176
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.80 E-value=7.1 Score=39.07 Aligned_cols=37 Identities=22% Similarity=0.264 Sum_probs=24.6
Q ss_pred ccccccccccc-cccc-cCc-eecCCCCccchhhHHHHHH
Q 008947 114 SSTVMCDICME-EVAG-DKA-TKMDCGHCFCNDCWTEHFI 150 (548)
Q Consensus 114 ~~~~~C~IC~e-~~~~-~~~-~~l~CgH~fC~~C~~~yl~ 150 (548)
....++++++. +... .++ ..-.|||.||..|-.-++.
T Consensus 93 ~~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~ 132 (271)
T COG5574 93 NREETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSI 132 (271)
T ss_pred ccccccccccCcccccccccceeeecccccchhhhHHHHH
Confidence 34578999988 3221 233 3338999999999665554
No 177
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=43.76 E-value=19 Score=36.65 Aligned_cols=46 Identities=28% Similarity=0.617 Sum_probs=35.6
Q ss_pred cccccccccccccc--cCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 115 STVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
....||||.+.+.. ..+..++|||..-..|+..++.. . +.||. |..
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 44669999998432 34566799999999999998764 2 78998 877
No 178
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=43.52 E-value=20 Score=26.19 Aligned_cols=33 Identities=21% Similarity=0.462 Sum_probs=22.7
Q ss_pred cccccccccccCceecCCCC-----ccchhhHHHHHHh
Q 008947 119 CDICMEEVAGDKATKMDCGH-----CFCNDCWTEHFIV 151 (548)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH-----~fC~~C~~~yl~~ 151 (548)
|-||++....+.+...||+- .....|+..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 67999986655555567652 5788999999987
No 179
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=42.83 E-value=8.3 Score=38.90 Aligned_cols=28 Identities=29% Similarity=0.670 Sum_probs=21.5
Q ss_pred CcCCCCCCcceee-cCCCCceEe-cccccc
Q 008947 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (548)
Q Consensus 276 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 303 (548)
|.+||+|+..+-+ .-+=|...| +|+|+|
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 5789999988875 446777888 588776
No 180
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.57 E-value=9.5 Score=42.58 Aligned_cols=36 Identities=25% Similarity=0.719 Sum_probs=28.2
Q ss_pred ccccccccccccc--cCceecCCCCccchhhHHHHHHh
Q 008947 116 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 116 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~ 151 (548)
-..|+||+..+-. -.++++.|||..|+-|.+.-...
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 3679999877532 36789999999999999876553
No 181
>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=42.56 E-value=18 Score=26.64 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=17.1
Q ss_pred CcCCC--CCCcceeecCCCCceEe-cccc
Q 008947 276 TKPCP--KCHKPVEKNGGCNLVSC-ICGQ 301 (548)
Q Consensus 276 tK~CP--kC~~~IEKn~GCnhMtC-~C~~ 301 (548)
-+.|| .|+.-+--..--+..+| +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 47899 99987754444466788 7874
No 182
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=42.42 E-value=31 Score=25.69 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 008947 53 EDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (548)
Q Consensus 53 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~ 89 (548)
+.|..++...|++..-+...|...+||.++-+..|.+
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5788999999999999999999999999999999875
No 183
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=41.33 E-value=1.1e+02 Score=23.96 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 008947 49 AAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (548)
Q Consensus 49 ~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~ 89 (548)
..|.+.|..++...|++..-+..+|...+||.+.-+..|.+
T Consensus 10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45788899999999999999999999999999998888874
No 184
>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=41.17 E-value=25 Score=22.80 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=12.9
Q ss_pred CCCCCCcceeecCCCCceEe
Q 008947 278 PCPKCHKPVEKNGGCNLVSC 297 (548)
Q Consensus 278 ~CPkC~~~IEKn~GCnhMtC 297 (548)
.||.|+..+.+..|=-+++|
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 49999999999888666666
No 185
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.82 E-value=21 Score=41.18 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=23.1
Q ss_pred cCCCCCCcceeecCCCCceEe-ccccc-----cccccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~ 310 (548)
-.||+|..++.--..=|.+.| .||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 478888887763222356888 48875 58888765
No 186
>PF12959 DUF3848: Protein of unknown function (DUF3848); InterPro: IPR024380 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences[].
Probab=40.81 E-value=1.1e+02 Score=26.16 Aligned_cols=49 Identities=24% Similarity=0.277 Sum_probs=38.9
Q ss_pred eeCHHHHHH-----HHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhc
Q 008947 41 VITRESLLA-----AQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVEN 90 (548)
Q Consensus 41 vlt~~~l~~-----~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~ 90 (548)
..+|++|+. .++++|-.+++-+.++...|.+||. ..=-.+.|++.|...
T Consensus 23 ~qpPeeIl~~AYEy~VkeDi~m~~ee~~l~~~qa~ALl~-sp~PL~~iY~~w~~~ 76 (101)
T PF12959_consen 23 SQPPEEILNHAYEYTVKEDILMAMEELELPDQQAKALLK-SPSPLADIYREWEKK 76 (101)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHc-CCChHHHHHHHHHhc
Confidence 357788876 5788999999999999999999995 444567788888753
No 187
>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=39.74 E-value=17 Score=28.42 Aligned_cols=38 Identities=21% Similarity=0.514 Sum_probs=19.6
Q ss_pred ccccccccccccccccCce--ecCCCCccchhhHHHHHHh
Q 008947 114 SSTVMCDICMEEVAGDKAT--KMDCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~--~l~CgH~fC~~C~~~yl~~ 151 (548)
.+...|.+|...|...... --.||+.||.+|....+..
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~ 46 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPL 46 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcc
Confidence 4557899999998542211 1279999999999776543
No 188
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=38.86 E-value=15 Score=37.16 Aligned_cols=32 Identities=28% Similarity=0.744 Sum_probs=25.7
Q ss_pred cCCCCCCcceeecCCCCceEe--cccccccccccccccCCC
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGATGRDH 315 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC--~C~~~FCw~C~~~~~~~H 315 (548)
-+|--|.-.|- +-| .|||-||++|-..+-..|
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~q 59 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQ 59 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCC
Confidence 57888888887 889 499999999988754444
No 189
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.77 E-value=18 Score=41.77 Aligned_cols=40 Identities=20% Similarity=0.571 Sum_probs=30.7
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
..|..|--++. -.++...|||.|...|+. ++ .-.||. |..
T Consensus 841 skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~---~~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK---EDKCPK--CLP 880 (933)
T ss_pred eeecccCCccc-cceeeeecccHHHHHhhc--------cC---cccCCc--cch
Confidence 57999987764 245677999999999998 33 357987 776
No 190
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.14 E-value=18 Score=35.79 Aligned_cols=37 Identities=14% Similarity=0.223 Sum_probs=30.9
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhcc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE 155 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~ 155 (548)
-.|+.|+.++ .+++..+=||.||++|+-+||..+-++
T Consensus 44 dcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 44 DCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 4688999886 377888889999999999999887654
No 191
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.50 E-value=16 Score=38.14 Aligned_cols=43 Identities=26% Similarity=0.627 Sum_probs=28.8
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
....|.||.+.. .+...++|||.-| |.--+- ..+.||. |...+
T Consensus 304 ~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 304 QPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCceEEecCCc--cceeeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 446799999985 3577789999866 533321 1245998 76543
No 192
>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=37.47 E-value=28 Score=25.67 Aligned_cols=26 Identities=35% Similarity=0.699 Sum_probs=17.7
Q ss_pred cCCCCCCcceeecCCCC--------ceEeccccc
Q 008947 277 KPCPKCHKPVEKNGGCN--------LVSCICGQA 302 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCn--------hMtC~C~~~ 302 (548)
-.||+|+.-.--|++=+ +=+|+||..
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 68999998776665433 236777764
No 193
>PRK12495 hypothetical protein; Provisional
Probab=37.21 E-value=24 Score=34.51 Aligned_cols=17 Identities=24% Similarity=0.718 Sum_probs=15.1
Q ss_pred CcCCCCCCcceeecCCC
Q 008947 276 TKPCPKCHKPVEKNGGC 292 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GC 292 (548)
.+.||.|+.||-+..||
T Consensus 42 a~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ 58 (226)
T ss_pred hhhcccccCcccCCCCe
Confidence 58999999999988887
No 194
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=36.95 E-value=21 Score=32.14 Aligned_cols=51 Identities=25% Similarity=0.534 Sum_probs=37.5
Q ss_pred cccccccccccccccCcee--cCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 115 STVMCDICMEEVAGDKATK--MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~--l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
.-.+|.||-|....+.... --||-..|.-|....|...- ....||. |+..+
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSF 131 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSF 131 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--ccccc
Confidence 5689999999854222222 25999999999999998753 3468998 88755
No 195
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=36.91 E-value=24 Score=40.34 Aligned_cols=49 Identities=33% Similarity=0.645 Sum_probs=36.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
..+.|.||.-.+.....+...|+|.-..+|...||.. |. .||. ||+..+
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~----gd----~Cps-GCGC~C 1075 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT----GD----VCPS-GCGCHC 1075 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc----CC----cCCC-CCCcCc
Confidence 4577899877776666677799999999999999986 22 6875 344433
No 196
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=36.90 E-value=34 Score=27.01 Aligned_cols=31 Identities=32% Similarity=0.623 Sum_probs=24.1
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCccccC
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~ 241 (548)
..|| +|++...+-+.....|+|. ||...+..
T Consensus 20 VkCp---dC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 20 VKCP---DCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EECC---CCCCEEEEeccCceEEEecccccEEEec
Confidence 5788 8999877666666779997 99987754
No 197
>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=36.59 E-value=28 Score=30.16 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=16.4
Q ss_pred cCCCCCCcceeecCCCCceEec-ccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~~F 303 (548)
-+||+|+.-.-=..|= .+.|. |+|+|
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCC-eeECccccccc
Confidence 5899999876655553 35563 55554
No 198
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=36.43 E-value=19 Score=38.66 Aligned_cols=6 Identities=0% Similarity=-0.009 Sum_probs=2.5
Q ss_pred HHHHHH
Q 008947 346 YMHYHN 351 (548)
Q Consensus 346 y~~y~~ 351 (548)
|..|+.
T Consensus 407 ~rk~C~ 412 (458)
T PF10446_consen 407 WRKHCR 412 (458)
T ss_pred HHHHHH
Confidence 344443
No 199
>PRK11827 hypothetical protein; Provisional
Probab=36.32 E-value=29 Score=26.89 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=17.1
Q ss_pred cCCCCCCcceeecCCCCceEec-ccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCI-CGQ 301 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~-C~~ 301 (548)
-.||.|+.+++-..+=+...|+ |+-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 5899999998865444556663 553
No 200
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.18 E-value=26 Score=30.08 Aligned_cols=27 Identities=26% Similarity=0.693 Sum_probs=15.3
Q ss_pred CcCCCCCCcce---eecCCCCceEe-ccccc
Q 008947 276 TKPCPKCHKPV---EKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 276 tK~CPkC~~~I---EKn~GCnhMtC-~C~~~ 302 (548)
.-.||+|+... ....|=-|..| .||+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 35799998322 22234456666 36654
No 201
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=36.17 E-value=32 Score=26.99 Aligned_cols=14 Identities=43% Similarity=0.949 Sum_probs=11.0
Q ss_pred CCcCCCCCCcceee
Q 008947 275 HTKPCPKCHKPVEK 288 (548)
Q Consensus 275 ~tK~CPkC~~~IEK 288 (548)
+.|+||.|+..+..
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 46999999977654
No 202
>cd07621 BAR_SNX5_6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Members of this subfamily include SNX5, SNX6, the mammalian SNX32, and similar proteins. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. The function of SNX32 is still unknown. BAR domain
Probab=35.92 E-value=4.4e+02 Score=25.98 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 008947 436 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDL 495 (548)
Q Consensus 436 fe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l 495 (548)
=|..|.+.+..-|.+|+...+++..+....+.++|.-++.++..--.|-+..+..+.+-|
T Consensus 156 AE~~~~~a~~~Fe~iS~~~k~El~rF~~~Rv~~fk~~lve~aE~~ik~Ak~~~~~l~~~~ 215 (219)
T cd07621 156 AEAAQQEACEKFESMSESAKQELLDFKTRRVAAFRKNLVELAELEIKHAKAQIQLLKNCL 215 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455778899999999999999998888888999999999999999888888888877544
No 203
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=35.82 E-value=11 Score=42.86 Aligned_cols=51 Identities=25% Similarity=0.609 Sum_probs=38.2
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchH
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~ 175 (548)
..+|+||+..+- ++..+.|.|.||..||..-+...-. ...||. |+..++..
T Consensus 21 ~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKR 71 (684)
T ss_pred hccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhh
Confidence 478999999863 5578899999999999988776332 467877 77554433
No 204
>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=35.58 E-value=25 Score=22.86 Aligned_cols=24 Identities=29% Similarity=0.778 Sum_probs=12.2
Q ss_pred cCCCCCCcceee--cCCCCceEe-ccc
Q 008947 277 KPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 277 K~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
++||+|..+|++ .+|=+...| +|.
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 589999999875 334444555 353
No 205
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=35.54 E-value=62 Score=38.08 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=14.8
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 008947 68 HARTLLIHYRWDVEKLLAVL 87 (548)
Q Consensus 68 ~a~~LL~~~~W~~~~l~~~~ 87 (548)
.++..++|||-.+=.|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 57778888877777777765
No 206
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.53 E-value=27 Score=34.86 Aligned_cols=53 Identities=17% Similarity=0.362 Sum_probs=38.3
Q ss_pred cccccccccccccccCce---ecCCC-----CccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 115 STVMCDICMEEVAGDKAT---KMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~---~l~Cg-----H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
..-.|=|||.+-. ++.. .-||. |-....|+..|+..+-..+...++.||+ |..
T Consensus 19 ~eR~CWiCF~Tde-Dn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqT 79 (293)
T KOG3053|consen 19 LERCCWICFATDE-DNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQT 79 (293)
T ss_pred cceeEEEEeccCc-ccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcc
Confidence 4568999998743 2222 22664 5688999999999887644456899999 886
No 207
>PLN02189 cellulose synthase
Probab=35.41 E-value=23 Score=42.20 Aligned_cols=59 Identities=27% Similarity=0.581 Sum_probs=42.3
Q ss_pred cCCCCCCCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCccee
Q 008947 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
-|. -|+--+....+....|-|. |+...|..|-+- . .+...+.||.|+....
T Consensus 36 ~C~---iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey----------e---------------r~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCE---ICGDEIGLTVDGDLFVACNECGFPVCRPCYEY----------E---------------RREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccc---ccccccCcCCCCCEEEeeccCCCccccchhhh----------h---------------hhcCCccCcccCCchh
Confidence 565 6888777666666779998 999999998631 0 0123478999999888
Q ss_pred ecCCCCce
Q 008947 288 KNGGCNLV 295 (548)
Q Consensus 288 Kn~GCnhM 295 (548)
+--|++.+
T Consensus 88 r~kgs~~v 95 (1040)
T PLN02189 88 RLKGSPRV 95 (1040)
T ss_pred hccCCCCc
Confidence 66666554
No 208
>PHA02926 zinc finger-like protein; Provisional
Probab=35.35 E-value=38 Score=33.28 Aligned_cols=35 Identities=31% Similarity=0.767 Sum_probs=23.1
Q ss_pred cCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCccee
Q 008947 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (548)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 287 (548)
+|++.||+.|-..|.. ... + ....+.||-|+....
T Consensus 196 ~CnHsFCl~CIr~Wr~------------~r~-~-------~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 196 SCNHIFCITCINIWHR------------TRR-E-------TGASDNCPICRTRFR 230 (242)
T ss_pred CCCchHHHHHHHHHHH------------hcc-c-------cCcCCcCCCCcceee
Confidence 5999999999765432 110 0 012378999998765
No 209
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=35.28 E-value=16 Score=30.33 Aligned_cols=35 Identities=29% Similarity=0.503 Sum_probs=28.9
Q ss_pred cCCCCCCcceeecCCCCceEecccccccccccccccCC
Q 008947 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRD 314 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~~~~ 314 (548)
..||.|+.| ...|--+.+.|++.|=..|...|-..
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 468888887 46788888899999999999997654
No 210
>PF14149 YhfH: YhfH-like protein
Probab=35.14 E-value=3.5 Score=28.63 Aligned_cols=26 Identities=31% Similarity=0.790 Sum_probs=20.4
Q ss_pred hCCcCCCCCCcceeecCCCCceEe-cc
Q 008947 274 VHTKPCPKCHKPVEKNGGCNLVSC-IC 299 (548)
Q Consensus 274 ~~tK~CPkC~~~IEKn~GCnhMtC-~C 299 (548)
...|.||.|+..|+--.-|-.++| +|
T Consensus 11 Lp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 346999999999987777777777 45
No 211
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.00 E-value=25 Score=41.70 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=24.1
Q ss_pred hCCcCCCCCCcceeecCCCCceEec-ccc-----ccccccccc
Q 008947 274 VHTKPCPKCHKPVEKNGGCNLVSCI-CGQ-----AFCWLCGGA 310 (548)
Q Consensus 274 ~~tK~CPkC~~~IEKn~GCnhMtC~-C~~-----~FCw~C~~~ 310 (548)
...+.||.|+... ....|. ||. .||-.|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCc
Confidence 4568999999884 447894 985 499999776
No 212
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.79 E-value=14 Score=40.36 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=19.2
Q ss_pred CcCCCCCCcceeecCCCCceEe--ccccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGA 310 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC--~C~~~FCw~C~~~ 310 (548)
-..||-|-.+-. .-+ .|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 378999987655 334 2777777777644
No 213
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=33.74 E-value=29 Score=35.25 Aligned_cols=25 Identities=44% Similarity=1.075 Sum_probs=17.5
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 3799999999986 566444455 354
No 214
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=33.59 E-value=31 Score=30.23 Aligned_cols=25 Identities=36% Similarity=0.830 Sum_probs=18.3
Q ss_pred cCCCCCCcceee----cCCCCceEe-cccccc
Q 008947 277 KPCPKCHKPVEK----NGGCNLVSC-ICGQAF 303 (548)
Q Consensus 277 K~CPkC~~~IEK----n~GCnhMtC-~C~~~F 303 (548)
+.||+|+.++.- .++ -+.| +||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~--~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGG--KLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCc--EEECCCCCcch
Confidence 689999987764 344 6888 488764
No 215
>PHA02929 N1R/p28-like protein; Provisional
Probab=33.12 E-value=18 Score=36.03 Aligned_cols=38 Identities=24% Similarity=0.407 Sum_probs=26.3
Q ss_pred CcCCCCCCcceeecCCCC---ceEecccccccccccccccC
Q 008947 276 TKPCPKCHKPVEKNGGCN---LVSCICGQAFCWLCGGATGR 313 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCn---hMtC~C~~~FCw~C~~~~~~ 313 (548)
...||-|.-.+.....-+ -+.-.|+|.||..|...|..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 478999998876543222 13346888999999888754
No 216
>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=32.98 E-value=25 Score=31.42 Aligned_cols=25 Identities=12% Similarity=0.215 Sum_probs=15.6
Q ss_pred cCCCCCCcceeecCCCCceEe-ccccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~~ 302 (548)
+.||+|++..---.- +-++| +||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCc
Confidence 679999876542111 55777 47665
No 217
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=32.86 E-value=15 Score=27.88 Aligned_cols=44 Identities=23% Similarity=0.553 Sum_probs=30.7
Q ss_pred cccccccccccccCceecCCC--CccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
..|..|-.+++.+..-..-|. ..||.+|-...+.. .||. |+..+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~----------~CPN--CgGel 51 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG----------VCPN--CGGEL 51 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC----------cCcC--CCCcc
Confidence 358888888876654444555 47999998887642 6888 77644
No 218
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=32.76 E-value=15 Score=31.14 Aligned_cols=9 Identities=22% Similarity=0.139 Sum_probs=3.5
Q ss_pred HHHHHHHHc
Q 008947 54 DLRRVMELL 62 (548)
Q Consensus 54 ~i~~v~~~l 62 (548)
-+..|...|
T Consensus 52 ~~~~v~rYl 60 (101)
T PF09026_consen 52 YFTMVKRYL 60 (101)
T ss_dssp HHHHHHHHH
T ss_pred hcchHhhhh
Confidence 333444333
No 219
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.42 E-value=30 Score=35.14 Aligned_cols=25 Identities=40% Similarity=1.060 Sum_probs=20.2
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
-++|+.|+.+|+| -+|=+-.+| .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4899999999997 577777777 475
No 220
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=32.33 E-value=5e+02 Score=25.58 Aligned_cols=59 Identities=17% Similarity=0.200 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 008947 436 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIEND 494 (548)
Q Consensus 436 fe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~ 494 (548)
-|..|.+.+..-|.+|+....++..+...-+..+|.-++.++...-.+-+.-|.-+.+-
T Consensus 155 aE~~~~~a~~~Fe~IS~~aK~El~rF~~~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~~~~ 213 (218)
T cd07662 155 AETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQLLQSC 213 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47788889999999999999888877667788888888888887777777766666543
No 221
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=32.06 E-value=2e+02 Score=29.29 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 008947 466 VMEIRMQVINLSVITDTLCKKMYE 489 (548)
Q Consensus 466 i~~~k~~~~~l~~~~~~~~~~l~~ 489 (548)
+.+.|.+|.+|..++++-..+|.+
T Consensus 119 LKEARkEIkQLkQvieTmrssL~e 142 (305)
T PF15290_consen 119 LKEARKEIKQLKQVIETMRSSLAE 142 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhch
Confidence 444455555555555544444443
No 222
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=31.98 E-value=48 Score=28.23 Aligned_cols=27 Identities=37% Similarity=0.795 Sum_probs=17.4
Q ss_pred ccCCCCCCCCceEEeccCce-eeeecc-CCCc
Q 008947 208 KWCPSTPHCGNAIRVEEVEV-CEVECA-CGAQ 237 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~~ 237 (548)
.+|| .|++.+.++.+.. ..+.|+ |++.
T Consensus 2 ~FCP---~Cgn~Live~g~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP---TCGNMLIVESGESCNRFSCRTCPYV 30 (105)
T ss_pred cccC---CCCCEEEEecCCeEeeEEcCCCCce
Confidence 4788 7999999876543 344554 5443
No 223
>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=31.69 E-value=45 Score=25.27 Aligned_cols=27 Identities=41% Similarity=0.815 Sum_probs=20.1
Q ss_pred cCCCCCCCCceEEecc-Cceeeeecc-CCCcc
Q 008947 209 WCPSTPHCGNAIRVEE-VEVCEVECA-CGAQF 238 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~-~~~~~v~C~-Cg~~f 238 (548)
-|| .|+.-|.+.+ .....+.|+ ||..+
T Consensus 4 ~CP---~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP---DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC---CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 587 7999988765 234568998 98875
No 224
>KOG2417 consensus Predicted G-protein coupled receptor [Signal transduction mechanisms]
Probab=31.45 E-value=4.3e+02 Score=27.98 Aligned_cols=14 Identities=7% Similarity=-0.180 Sum_probs=7.7
Q ss_pred chhHHHHHHHHHHH
Q 008947 386 DFSWVTNGLYRLFR 399 (548)
Q Consensus 386 ~~~~l~~a~~~l~~ 399 (548)
+-+|++.-+..+.+
T Consensus 227 ~pSff~r~w~~~~~ 240 (462)
T KOG2417|consen 227 EPSFFRRFWGMFSS 240 (462)
T ss_pred CCcHHHHHHHHHHH
Confidence 34666665555544
No 225
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=31.32 E-value=64 Score=37.12 Aligned_cols=41 Identities=22% Similarity=0.273 Sum_probs=25.7
Q ss_pred CeeeeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHH
Q 008947 38 STKVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEK 82 (548)
Q Consensus 38 ~~~vlt~~~l~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~ 82 (548)
.++.|++.++.+..++.-..-.+-+ +.-..||.+-+|..+.
T Consensus 412 pf~~l~ksq~~kl~k~q~k~y~de~----dyr~kl~~kkq~ke~~ 452 (763)
T TIGR00993 412 PFKPLTKAQMAKLSKEQRKAYLEEY----DYRVKLLQKKQWREEL 452 (763)
T ss_pred CCccccHHHHHHHhHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 3567888887766554433322222 3556788888997665
No 226
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.77 E-value=39 Score=25.65 Aligned_cols=33 Identities=27% Similarity=0.824 Sum_probs=25.1
Q ss_pred cccccccccccc-ccCceec-CCCCccchhhHHHH
Q 008947 116 TVMCDICMEEVA-GDKATKM-DCGHCFCNDCWTEH 148 (548)
Q Consensus 116 ~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~C~~~y 148 (548)
...|++|-+.+. .++.+.. .||-.|.++||...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 356999999984 3455544 89999999999653
No 227
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.60 E-value=25 Score=27.08 Aligned_cols=6 Identities=67% Similarity=2.084 Sum_probs=3.1
Q ss_pred CCCCCC
Q 008947 278 PCPKCH 283 (548)
Q Consensus 278 ~CPkC~ 283 (548)
.||+|+
T Consensus 29 ~CPnCG 34 (61)
T COG2888 29 PCPNCG 34 (61)
T ss_pred eCCCCC
Confidence 455555
No 228
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=30.55 E-value=2.8e+02 Score=22.17 Aligned_cols=48 Identities=25% Similarity=0.362 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 008947 434 HLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKK 486 (548)
Q Consensus 434 ~lfe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~ 486 (548)
.-|+.+++..+.....|...++.. ..+-..++.++.+|+.-|..+=+.
T Consensus 17 ~~y~~q~~~Wq~sy~~Lq~~~~~t-----~~~~a~L~~qv~~Ls~qv~~Ls~q 64 (70)
T PF04899_consen 17 QSYEKQQQEWQSSYADLQHMFEQT-----SQENAALSEQVNNLSQQVQRLSEQ 64 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888888888888888888753 233557778888888777554433
No 229
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=30.44 E-value=35 Score=34.71 Aligned_cols=25 Identities=40% Similarity=1.024 Sum_probs=18.1
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 3799999999986 566555556 365
No 230
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=30.39 E-value=50 Score=32.12 Aligned_cols=15 Identities=33% Similarity=0.904 Sum_probs=12.2
Q ss_pred ccCCCCCCCCceEEec
Q 008947 208 KWCPSTPHCGNAIRVE 223 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~ 223 (548)
.-|| .|+|.++|...
T Consensus 139 IACP-RpnCkRiInL~ 153 (275)
T KOG4684|consen 139 IACP-RPNCKRIINLD 153 (275)
T ss_pred eccC-CCCcceeeecC
Confidence 4799 69999998754
No 231
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=30.29 E-value=46 Score=22.48 Aligned_cols=12 Identities=33% Similarity=0.515 Sum_probs=8.9
Q ss_pred CcCCCCCCccee
Q 008947 276 TKPCPKCHKPVE 287 (548)
Q Consensus 276 tK~CPkC~~~IE 287 (548)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 368998987655
No 232
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.27 E-value=35 Score=34.65 Aligned_cols=24 Identities=42% Similarity=1.012 Sum_probs=17.4
Q ss_pred CcCCCCCCcceee--cCCCCceEe-cc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-IC 299 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C 299 (548)
-++||.|+.+|+| .+|=.-.+| .|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 3699999999996 466555555 35
No 233
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.23 E-value=45 Score=34.29 Aligned_cols=51 Identities=18% Similarity=0.482 Sum_probs=35.3
Q ss_pred cccccccccccccc-cCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 115 STVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 115 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
+.|+|||=-+.... +.|+.|.|||.+=+.=+...- ++|. ..++||- |+..-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~-~~FKCPY--CP~~~ 386 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGV-LSFKCPY--CPEMS 386 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCc-EEeeCCC--CCcch
Confidence 56899997666433 456788999998776554432 3454 5899998 87643
No 234
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.95 E-value=35 Score=34.67 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=18.1
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
.++||+|+.+|++ .+|=.-.+| .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 4799999999986 566555555 354
No 235
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=29.94 E-value=5.2e+02 Score=24.98 Aligned_cols=95 Identities=15% Similarity=0.295 Sum_probs=51.7
Q ss_pred hccccchhHHHHHHHHHHHHhHhhhccceeeeeccCccccccccChHHHHHhHHHHHHHHHHHHHHHHH---HHHHhccc
Q 008947 381 ESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEK---LSKFLEEP 457 (548)
Q Consensus 381 ~~~~~~~~~l~~a~~~l~~~R~~L~~sy~~~yy~~~~~~~~~~~~~~e~~~~~~lfe~~Q~~lE~~~E~---L~~~le~~ 457 (548)
..+++++.....+++.+++.|.+..+.|... ......+... .++++|...+. ..+.+..+
T Consensus 97 ~e~LkEy~~ya~slk~vlk~r~~~q~~~e~~--------------~~~L~~k~~~---l~~~ve~a~~~~e~f~~~~~~E 159 (201)
T cd07622 97 ADQLKEYLFFADSLRAVCKKHELLQYDLEKA--------------EDALANKKQQ---GEEAVKEAKDELNEFVKKALED 159 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 3457788888889999888777777655332 1111112222 22222222222 22233344
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008947 458 FDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 492 (548)
Q Consensus 458 ~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (548)
+..+...+..++|.-+.+++..=-.++++++..-+
T Consensus 160 ~~rF~~~K~~dlk~~l~~~A~~qi~~~~~~~~~W~ 194 (201)
T cd07622 160 VERFKKQKVRDLKEILISYAKLQIKLAKKGLQTWT 194 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455667777777777766666666665544
No 236
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.47 E-value=37 Score=25.34 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=23.3
Q ss_pred ccccccccccccCceecCCCCccchhhHHHH
Q 008947 118 MCDICMEEVAGDKATKMDCGHCFCNDCWTEH 148 (548)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 148 (548)
.|+||-.....-..+.+.=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999998765444667777 8999999776
No 237
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.37 E-value=36 Score=34.73 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=18.8
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 4799999999986 567555666 364
No 238
>PRK10445 endonuclease VIII; Provisional
Probab=29.24 E-value=38 Score=34.24 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=18.4
Q ss_pred CcCCCCCCcceee--cCCCCceEe-ccc
Q 008947 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (548)
Q Consensus 276 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 300 (548)
-++||.|+.+|++ .+|=.-.+| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 4799999999986 566555566 364
No 239
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=29.23 E-value=5.4e+02 Score=24.99 Aligned_cols=50 Identities=16% Similarity=0.202 Sum_probs=29.1
Q ss_pred HHHhhhHHHHHHHHHHHHHHHHHHhhhhhccccch---hHHHHHHHHHHHHhH
Q 008947 353 YKAHTDSFKLESKLKETVLEKVSISEERESRLRDF---SWVTNGLYRLFRSRR 402 (548)
Q Consensus 353 ~~~h~~s~k~e~~l~~~i~~k~~~~~~~~~~~~~~---~~l~~a~~~l~~~R~ 402 (548)
|..|..++..+.+-.+.+.+.+.++......+.++ .|...|++...++.-
T Consensus 38 ~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ag~~~~a~QEyvEA~~ 90 (204)
T COG2178 38 FLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPELYFAGFVTTALQEYVEATL 90 (204)
T ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhcchHHHHHHHHH
Confidence 45677666555444444555555555433333333 468889988888743
No 240
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.21 E-value=33 Score=24.12 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=17.2
Q ss_pred CCCCCCcceeecCCCCceEecccccccccccccc
Q 008947 278 PCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (548)
Q Consensus 278 ~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~ 311 (548)
.||+|+..++...- ..+. ..-|-.|++.|
T Consensus 1 ~CP~C~~~l~~~~~-~~~~----id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDVE----IDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEE-CCEE----EEECCCCCeEE
Confidence 59999998775332 1121 23455677775
No 241
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=29.14 E-value=31 Score=41.33 Aligned_cols=56 Identities=20% Similarity=0.517 Sum_probs=40.0
Q ss_pred CCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCC
Q 008947 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 293 (548)
-||--|....+....|-|. |+...|..|-+- . .+...+.||.|+....+--||.
T Consensus 22 ICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEY----------E---------------r~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 22 ICGDNVGKTVDGEPFVACDVCAFPVCRPCYEY----------E---------------RKDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred ecccccCcCCCCCEEEEeccCCCccccchhhh----------h---------------hhcCCccCCccCCchhhhcCCC
Confidence 5887777766666789998 999999998631 0 1123478999988887665665
Q ss_pred ce
Q 008947 294 LV 295 (548)
Q Consensus 294 hM 295 (548)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 54
No 242
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=28.72 E-value=1.8e+02 Score=29.91 Aligned_cols=31 Identities=19% Similarity=0.316 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhhHHHHHH
Q 008947 334 KKTERAKRELYRYMHYHNRYKAHTDSFKLES 364 (548)
Q Consensus 334 ~~~~~~k~~l~ry~~y~~r~~~h~~s~k~e~ 364 (548)
.+..+|-..|+||.+-++|-.+....+.++.
T Consensus 151 ~ranQAi~TLEkYk~~Ld~~~~~L~~lEled 181 (349)
T COG1623 151 SRANQAIQTLEKYKTVLDRVLNQLNLLELED 181 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhHHHhh
Confidence 5677888999999999999888777776664
No 243
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.03 E-value=64 Score=22.86 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=8.2
Q ss_pred cCCCCCCc-ceee
Q 008947 277 KPCPKCHK-PVEK 288 (548)
Q Consensus 277 K~CPkC~~-~IEK 288 (548)
..||.|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 57888877 5554
No 244
>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=27.43 E-value=25 Score=26.27 Aligned_cols=25 Identities=28% Similarity=0.647 Sum_probs=12.4
Q ss_pred cCCCCCCcceeecCCC--CceEe-cccc
Q 008947 277 KPCPKCHKPVEKNGGC--NLVSC-ICGQ 301 (548)
Q Consensus 277 K~CPkC~~~IEKn~GC--nhMtC-~C~~ 301 (548)
-+|++|++.+-+.++= -.|.| +|+.
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 3566666665553221 23555 4553
No 245
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.33 E-value=49 Score=23.90 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=5.3
Q ss_pred cCCCCCCcce
Q 008947 277 KPCPKCHKPV 286 (548)
Q Consensus 277 K~CPkC~~~I 286 (548)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 4555555544
No 246
>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=27.28 E-value=24 Score=27.14 Aligned_cols=34 Identities=29% Similarity=0.698 Sum_probs=26.4
Q ss_pred cCCCCCCcceee--cCCCCceEe-ccccccccccccc
Q 008947 277 KPCPKCHKPVEK--NGGCNLVSC-ICGQAFCWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~IEK--n~GCnhMtC-~C~~~FCw~C~~~ 310 (548)
..||-|+...-- .+-=|+=+| .|+...|-+||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 579999987621 234688999 5999999999864
No 247
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.03 E-value=34 Score=27.35 Aligned_cols=43 Identities=26% Similarity=0.655 Sum_probs=29.8
Q ss_pred ccccccccccccCceecCCC--CccchhhHHHHHHhhhccCCccceecCcccccccc
Q 008947 118 MCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (548)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i 172 (548)
.|..|--+++++..-.+-|. |.||.+|-..-+. | .||. |+..+
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-----g-----~CPn--CGGel 51 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLH-----G-----LCPN--CGGEL 51 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-----C-----cCCC--CCchh
Confidence 47778777776555555554 8899999876543 2 5888 77644
No 248
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.97 E-value=30 Score=40.70 Aligned_cols=24 Identities=50% Similarity=1.297 Sum_probs=19.0
Q ss_pred cCCCCCCc-ceeecCCCCceEe-ccccc
Q 008947 277 KPCPKCHK-PVEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 277 K~CPkC~~-~IEKn~GCnhMtC-~C~~~ 302 (548)
-.||-|+. .||..|||| || .||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999986 788999997 67 47654
No 249
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=26.62 E-value=38 Score=40.89 Aligned_cols=14 Identities=36% Similarity=0.707 Sum_probs=5.5
Q ss_pred CCCCcceeecCCCC
Q 008947 280 PKCHKPVEKNGGCN 293 (548)
Q Consensus 280 PkC~~~IEKn~GCn 293 (548)
|+|-.-+--.+.|-
T Consensus 2282 ~kclfE~rn~g~~L 2295 (3015)
T KOG0943|consen 2282 GKCLFEVRNDGNCL 2295 (3015)
T ss_pred CcceEEEecCCcee
Confidence 44444333333343
No 250
>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=26.61 E-value=40 Score=24.14 Aligned_cols=41 Identities=27% Similarity=0.646 Sum_probs=19.6
Q ss_pred cccccccccccCc-eecCCCCccchhhHHHHHHhhhccCCccceecCc
Q 008947 119 CDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (548)
Q Consensus 119 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 165 (548)
|.+|-+.+..... ....|+=.+...|+..||...-. .+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~------~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSN------PKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-------B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCC------CCCcC
Confidence 6677776532211 11258888999999999987321 27886
No 251
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=26.57 E-value=62 Score=25.00 Aligned_cols=31 Identities=32% Similarity=0.618 Sum_probs=22.6
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCccccC
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~ 241 (548)
..|| +|++...+-+.....|.|. ||...+.-
T Consensus 12 VkCp---~C~n~q~vFsha~t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 12 VKCP---DCGNEQVVFSHASTVVRCLVCGKTLAEP 43 (59)
T ss_pred EECC---CCCCeEEEEecCCcEEECcccCCCcccC
Confidence 4687 8998876656556678997 88886653
No 252
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=26.50 E-value=31 Score=24.55 Aligned_cols=25 Identities=28% Similarity=0.711 Sum_probs=14.0
Q ss_pred CCCCceEEeccCceeeeecc-CCCccccCcCc
Q 008947 214 PHCGNAIRVEEVEVCEVECA-CGAQFCFSCLS 244 (548)
Q Consensus 214 p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~ 244 (548)
++|+.... ..+.|+ |+..||...+.
T Consensus 4 ~~C~~~~~------~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 4 PGCKKKDF------LPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp TTT--BCT------SHEE-TTTS-EE-TTTHS
T ss_pred CcCcCccC------CCeECCCCCcccCccccC
Confidence 56754332 247898 99999999764
No 253
>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=26.08 E-value=38 Score=26.65 Aligned_cols=17 Identities=24% Similarity=0.702 Sum_probs=12.3
Q ss_pred ccchhhHHHHHHhhhcc
Q 008947 139 CFCNDCWTEHFIVKINE 155 (548)
Q Consensus 139 ~fC~~C~~~yl~~~i~~ 155 (548)
-||++|+..|+...-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999887654
No 254
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.08 E-value=30 Score=31.79 Aligned_cols=95 Identities=15% Similarity=0.262 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCCCCCC--Cccccccccccccc
Q 008947 48 LAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPML--PLSSTVMCDICMEE 125 (548)
Q Consensus 48 ~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~--~~~~~~~C~IC~e~ 125 (548)
...++++|.+...-+|+..-.. .+-..=-|+.|.+.+. ++ ..|++.||.++....... .......|+-|-..
T Consensus 41 ~e~L~~~I~~aL~~~Gv~~V~V-~i~~~p~Wt~d~it~~----gr-~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s~ 114 (146)
T TIGR02159 41 LEVIRQDIRDAVRALGVEVVEV-STSLDPPWTTDWITED----AR-EKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGSA 114 (146)
T ss_pred HHHHHHHHHHHHHhcCCCeEEE-eEeeCCCCChHHCCHH----HH-HHHHhcCccCCCccCCCcccCCCCCCcCCCCCCC
Confidence 3344444444333346542111 1222345888876554 33 367788998775431111 01224799999886
Q ss_pred cc--ccCceecCCC-CccchhhHHHH
Q 008947 126 VA--GDKATKMDCG-HCFCNDCWTEH 148 (548)
Q Consensus 126 ~~--~~~~~~l~Cg-H~fC~~C~~~y 148 (548)
.. .+.+-+..|. ..+|++|..-|
T Consensus 115 ~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 115 DTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcEeecCCCChhhHHHhhhhhhCCcH
Confidence 43 2344456887 67899997543
No 255
>PLN02436 cellulose synthase A
Probab=26.02 E-value=43 Score=40.19 Aligned_cols=56 Identities=23% Similarity=0.527 Sum_probs=39.6
Q ss_pred CCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCC
Q 008947 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 293 (548)
-|+--|....+....|-|. |+...|..|-.- . .+...+.||.|+....+--|++
T Consensus 41 ICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey----------e---------------r~eg~~~Cpqckt~Y~r~kgs~ 95 (1094)
T PLN02436 41 ICGDEIELTVDGEPFVACNECAFPVCRPCYEY----------E---------------RREGNQACPQCKTRYKRIKGSP 95 (1094)
T ss_pred ccccccCcCCCCCEEEeeccCCCccccchhhh----------h---------------hhcCCccCcccCCchhhccCCC
Confidence 5777776666666779998 999999998631 0 0123478999998888666665
Q ss_pred ce
Q 008947 294 LV 295 (548)
Q Consensus 294 hM 295 (548)
.+
T Consensus 96 ~~ 97 (1094)
T PLN02436 96 RV 97 (1094)
T ss_pred Cc
Confidence 54
No 256
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=25.98 E-value=45 Score=31.85 Aligned_cols=24 Identities=38% Similarity=0.933 Sum_probs=19.4
Q ss_pred CCCCCCcceeecCCCCceEe-ccccc
Q 008947 278 PCPKCHKPVEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 278 ~CPkC~~~IEKn~GCnhMtC-~C~~~ 302 (548)
.||+|+.++.+ .+.|+|.| .|++.
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCPNCGNI 175 (189)
T ss_pred EccccCCceEE-CCCCEEECCCCCCE
Confidence 79999999987 44599999 59864
No 257
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.92 E-value=83 Score=29.24 Aligned_cols=32 Identities=28% Similarity=0.530 Sum_probs=19.2
Q ss_pred cCcccccCCCCCCCCceEEeccCceeeeecc-CCCc
Q 008947 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (548)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (548)
.++.+-.|| .|+.-+...+.-...+.|| ||..
T Consensus 105 ~~~~~Y~Cp---~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICP---NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECC---CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345566898 5876555444333356777 7765
No 258
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=25.85 E-value=52 Score=26.95 Aligned_cols=35 Identities=23% Similarity=0.493 Sum_probs=23.4
Q ss_pred ccccccccccc-ccC-ceec-CCCCccchhhHHHHHHh
Q 008947 117 VMCDICMEEVA-GDK-ATKM-DCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 117 ~~C~IC~e~~~-~~~-~~~l-~CgH~fC~~C~~~yl~~ 151 (548)
.+|+-|.-... .++ ++.- -|.|.|..-|+..++.+
T Consensus 32 ~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh
Confidence 45666654322 222 2222 69999999999999988
No 259
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=25.69 E-value=63 Score=32.94 Aligned_cols=35 Identities=23% Similarity=0.595 Sum_probs=25.3
Q ss_pred HHHHHHhCCcCCCCCCcceeecCCCCceEe-cccccc
Q 008947 268 TVNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (548)
Q Consensus 268 ~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 303 (548)
-..|...+ +-||+|+.+.+-..|=-.+.| .||+.+
T Consensus 104 l~~w~~~~-RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 104 LLEWYRSH-RFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHHhhC-cCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 34554443 899999999988777777788 487654
No 260
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=25.35 E-value=42 Score=34.89 Aligned_cols=32 Identities=25% Similarity=0.753 Sum_probs=24.2
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHH
Q 008947 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 147 (548)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~ 147 (548)
.+...|.||...+. -...+||+|..|.-|--.
T Consensus 59 Een~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~R 90 (493)
T COG5236 59 EENMNCQICAGSTT--YSARYPCGHQICHACAVR 90 (493)
T ss_pred cccceeEEecCCce--EEEeccCCchHHHHHHHH
Confidence 35678999998753 334569999999999544
No 261
>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=25.28 E-value=62 Score=23.92 Aligned_cols=47 Identities=17% Similarity=0.436 Sum_probs=24.4
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCcccccc
Q 008947 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 170 (548)
+.|+|-+..+. .......|.|.-|-| +..|+....+.+. .+||. |+.
T Consensus 3 L~CPls~~~i~-~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~---W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR-IPVRGKNCKHLQCFD-LESFLESNQRTPK---WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-S-SEEEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEE-eCccCCcCcccceEC-HHHHHHHhhccCC---eECcC--CcC
Confidence 56888887753 234456999998854 7788887665544 78998 754
No 262
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.21 E-value=66 Score=29.02 Aligned_cols=21 Identities=48% Similarity=1.211 Sum_probs=16.1
Q ss_pred CCCCceEEeccCceeeeeccCCCccccC
Q 008947 214 PHCGNAIRVEEVEVCEVECACGAQFCFS 241 (548)
Q Consensus 214 p~C~~~i~~~~~~~~~v~C~Cg~~fC~~ 241 (548)
|.|++..- .+.|.||..+|..
T Consensus 81 P~CGn~~~-------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 81 PHCGNQYA-------FAVCGCGKLFCID 101 (131)
T ss_pred CCCcChhc-------EEEecCCCEEEeC
Confidence 37876543 4789999999986
No 263
>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=25.13 E-value=91 Score=23.16 Aligned_cols=45 Identities=18% Similarity=0.410 Sum_probs=23.8
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhccCCccceecCccccccccchHHH
Q 008947 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~~~i 177 (548)
.|.||.|...++.. . +..++...=... ...+.||. |...+....+
T Consensus 2 ~f~CP~C~~~~~~~---~-----------L~~H~~~~H~~~-~~~v~CPi--C~~~~~~~l~ 46 (54)
T PF05605_consen 2 SFTCPYCGKGFSES---S-----------LVEHCEDEHRSE-SKNVVCPI--CSSRVTDNLI 46 (54)
T ss_pred CcCCCCCCCccCHH---H-----------HHHHHHhHCcCC-CCCccCCC--chhhhhhHHH
Confidence 58899998854311 1 223332221111 23689998 8765544333
No 264
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=24.77 E-value=44 Score=40.05 Aligned_cols=56 Identities=29% Similarity=0.671 Sum_probs=38.6
Q ss_pred CCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCC
Q 008947 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 293 (548)
-||--|....+....|-|. |+...|..|-.- - .+...+.||.|+.+..+--|++
T Consensus 20 iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyey-e------------------------~~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 20 VCGDEVGVKEDGQPFVACHVCGFPVCKPCYEY-E------------------------RSEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred ccccccCcCCCCCEEEEeccCCCccccchhhh-h------------------------hhcCCccCCccCCchhhhcCCC
Confidence 5776666666666789998 999999998631 0 1123478898888887655555
Q ss_pred ce
Q 008947 294 LV 295 (548)
Q Consensus 294 hM 295 (548)
.+
T Consensus 75 ~~ 76 (1044)
T PLN02915 75 RV 76 (1044)
T ss_pred Cc
Confidence 43
No 265
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.63 E-value=99 Score=28.23 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=13.3
Q ss_pred HHHHHcCCCHHHHHHHHH
Q 008947 57 RVMELLSLREHHARTLLI 74 (548)
Q Consensus 57 ~v~~~l~i~~~~a~~LL~ 74 (548)
.++..|||+....+.+|.
T Consensus 20 dLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 20 DLAELLGIKQKQLRKILY 37 (147)
T ss_pred HHHHHhCCCHHHHHHHHH
Confidence 455678888888877774
No 266
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=24.61 E-value=45 Score=33.15 Aligned_cols=22 Identities=27% Similarity=0.715 Sum_probs=11.8
Q ss_pred HHHHHHHHhCCcCCCCCCcc-eee
Q 008947 266 SETVNWITVHTKPCPKCHKP-VEK 288 (548)
Q Consensus 266 ~~~~~~i~~~tK~CPkC~~~-IEK 288 (548)
..+..|+..|. .||+|+.. +.+
T Consensus 22 VltE~Wv~~n~-yCP~Cg~~~L~~ 44 (254)
T PF06044_consen 22 VLTEDWVAENM-YCPNCGSKPLSK 44 (254)
T ss_dssp HHHHHHHHHH----TTT--SS-EE
T ss_pred HHHHHHHHHCC-cCCCCCChhHhh
Confidence 34668888775 89999976 665
No 267
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.37 E-value=79 Score=26.24 Aligned_cols=35 Identities=26% Similarity=0.511 Sum_probs=26.4
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCccccCcCcc
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSE 245 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~ 245 (548)
+.|| +|.+.-.+-+.....|.|. ||...|.-=+..
T Consensus 36 VkCp---~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK 71 (85)
T PTZ00083 36 VKCP---GCSQITTVFSHAQTVVLCGGCSSQLCQPTGGK 71 (85)
T ss_pred EECC---CCCCeeEEEecCceEEEccccCCEeeccCCCC
Confidence 5788 8998877666666779997 999988654443
No 268
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.25 E-value=44 Score=30.13 Aligned_cols=36 Identities=31% Similarity=0.742 Sum_probs=19.8
Q ss_pred CCcCCCCCCccee-ecCCCCceEec--cccccccccccc
Q 008947 275 HTKPCPKCHKPVE-KNGGCNLVSCI--CGQAFCWLCGGA 310 (548)
Q Consensus 275 ~tK~CPkC~~~IE-Kn~GCnhMtC~--C~~~FCw~C~~~ 310 (548)
..--||.|+...- -.-+|.+++|. =+..-|--|+..
T Consensus 76 g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred CCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCe
Confidence 3478999998743 22345555552 334445555543
No 269
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=24.21 E-value=35 Score=35.01 Aligned_cols=28 Identities=25% Similarity=0.776 Sum_probs=20.9
Q ss_pred CcCCCCCCcceeecCCCCceEec---cccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGA 310 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC~---C~~~FCw~C~~~ 310 (548)
...|-+|..+|- ++=| |++.||+.|...
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 468999999998 4443 777777777654
No 270
>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 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=23.82 E-value=50 Score=19.04 Aligned_cols=16 Identities=31% Similarity=0.793 Sum_probs=12.6
Q ss_pred cccCcCccCCCCCCch
Q 008947 238 FCFSCLSEAHSPCSCS 253 (548)
Q Consensus 238 fC~~C~~~~H~p~~C~ 253 (548)
.|+.|+..-|.-..|.
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 5899999999866553
No 272
>PF14353 CpXC: CpXC protein
Probab=23.60 E-value=36 Score=30.16 Aligned_cols=50 Identities=28% Similarity=0.606 Sum_probs=28.6
Q ss_pred eecCccccccccchHHHHHhhccCChhHHHHHHHHHHHHhhhcCcccccCCCCCCCCceEEec
Q 008947 161 IRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE 223 (548)
Q Consensus 161 i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~ 223 (548)
|+||. |+..+.......+-...+|++.++. ++..-....|| .||..+.+.
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~i--------l~g~l~~~~CP---~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEKI--------LDGSLFSFTCP---SCGHKFRLE 51 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHHH--------HcCCcCEEECC---CCCCceecC
Confidence 78998 8887665544333333345555432 22333445787 688776643
No 273
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.54 E-value=41 Score=29.37 Aligned_cols=28 Identities=29% Similarity=0.644 Sum_probs=18.2
Q ss_pred cccCCCCCCCCceEEeccCceeeeeccCCCccccCcCcc
Q 008947 207 VKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSE 245 (548)
Q Consensus 207 ~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~ 245 (548)
...|+ +|+..-. +.-+|+..+|..|+..
T Consensus 42 ~~~C~---~Cg~~~~--------~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCE---DCGHEKI--------VYNSCKNRHCPSCQAK 69 (111)
T ss_pred eeecC---CCCceEE--------ecCcccCcCCCCCCCh
Confidence 34676 5765433 2335999999999863
No 274
>KOG4759 consensus Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=23.47 E-value=7.3e+02 Score=25.14 Aligned_cols=67 Identities=18% Similarity=0.195 Sum_probs=46.8
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 008947 431 IKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLG 497 (548)
Q Consensus 431 ~~~~lfe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~ 497 (548)
....+|+...+.|-+--....+.+........++++.++..++.+|....-+....|++.-|.+|++
T Consensus 196 ~~~~~~ee~K~slr~ir~~~~kk~~k~~~~~~~D~vkkae~~l~~l~k~~v~~ld~llkskeKellk 262 (263)
T KOG4759|consen 196 VLKRYFEEYKQSLRKIRTKSIKKSKKNKKSLSEDEVKKAEAELQKLAKDAVNKLDDLLKSKEKELLK 262 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445565555555444444444444333336788999999999999999988888899888888774
No 275
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.21 E-value=68 Score=33.29 Aligned_cols=34 Identities=26% Similarity=0.754 Sum_probs=25.0
Q ss_pred cCCCCCCcc-----e--eecCCCCceEe-cccccc------ccccccc
Q 008947 277 KPCPKCHKP-----V--EKNGGCNLVSC-ICGQAF------CWLCGGA 310 (548)
Q Consensus 277 K~CPkC~~~-----I--EKn~GCnhMtC-~C~~~F------Cw~C~~~ 310 (548)
..||-|+.. | .-.+|=-++.| .|+++| |-.|+..
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 679999865 2 12467788999 599875 8889864
No 276
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=23.20 E-value=52 Score=22.60 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=15.3
Q ss_pred cchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 140 FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 140 fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
.|.+|+++|....-+-=....+.|+. |+-.
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr 30 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPR 30 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-S
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCC
Confidence 48899999876532211235688987 7643
No 277
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.04 E-value=99 Score=29.36 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=18.2
Q ss_pred cCcccccCCCCCCCCceEEeccCceeeeecc-CCCc
Q 008947 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (548)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (548)
.++.+-.|| .|+.-+...+.-...+.|| ||..
T Consensus 113 ~~~~~Y~Cp---~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 113 ENNMFFFCP---NCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred cCCCEEECC---CCCcEEeHHHHhhcCCcCCCCCCC
Confidence 344566898 5886666544322345665 6544
No 278
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=22.95 E-value=43 Score=40.43 Aligned_cols=19 Identities=26% Similarity=0.440 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 008947 435 LFEDQQQQLEANVEKLSKF 453 (548)
Q Consensus 435 lfe~~Q~~lE~~~E~L~~~ 453 (548)
-||.-|....+.+|+|...
T Consensus 2418 ~FEtKer~Fnka~EK~RnQ 2436 (3015)
T KOG0943|consen 2418 GFETKERKFNKAMEKLRNQ 2436 (3015)
T ss_pred ccchHHHHHHHHHHHHHhc
Confidence 4666666666666666543
No 279
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=22.81 E-value=5.8e+02 Score=27.53 Aligned_cols=91 Identities=23% Similarity=0.323 Sum_probs=55.4
Q ss_pred HHHHHHhHHHHHHHHHHHhhhHHHHHHH-HHHHHHHHHHHhhhhhccccchhHHHHHHHHHHH-HhHhhhccceeeeecc
Q 008947 338 RAKRELYRYMHYHNRYKAHTDSFKLESK-LKETVLEKVSISEERESRLRDFSWVTNGLYRLFR-SRRVLSYSYPFAFYMF 415 (548)
Q Consensus 338 ~~k~~l~ry~~y~~r~~~h~~s~k~e~~-l~~~i~~k~~~~~~~~~~~~~~~~l~~a~~~l~~-~R~~L~~sy~~~yy~~ 415 (548)
+||.++--...--.|++-|.+.++-+-. +.+.++.+-++.++ |+.-..+|.. ||.|..
T Consensus 122 rAKDSItSlKekt~~vnQHVq~LQseCsvlsEnLErrrQEaeE----------LEgyCsqLk~nCrkVt~---------- 181 (558)
T PF15358_consen 122 RAKDSITSLKEKTSRVNQHVQTLQSECSVLSENLERRRQEAEE----------LEGYCSQLKENCRKVTR---------- 181 (558)
T ss_pred ecccchhhHHHhhHHHHHHHHHHHHHhHHHHHHHHhhhhHHHH----------HHHHHHHHHHHHHHHhh----------
Confidence 3455554445566788899999887743 55555555444433 4444444443 344331
Q ss_pred CccccccccChHHHHHhHHHHHHHHHHHHHHHHHHHHHhccc
Q 008947 416 GEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEP 457 (548)
Q Consensus 416 ~~~~~~~~~~~~e~~~~~~lfe~~Q~~lE~~~E~L~~~le~~ 457 (548)
+-++.+.+.+.+..+-..||..+.-|..-|..+
T Consensus 182 ---------SVedaEiKtnvLkqnS~~LEekLr~lq~qLqdE 214 (558)
T PF15358_consen 182 ---------SVEDAEIKTNVLKQNSALLEEKLRYLQQQLQDE 214 (558)
T ss_pred ---------hHHHHHHHhcccccchHHHHHHHHHHHHHhccc
Confidence 112335777888888888888888777777643
No 280
>PLN02400 cellulose synthase
Probab=22.60 E-value=70 Score=38.57 Aligned_cols=56 Identities=27% Similarity=0.577 Sum_probs=38.8
Q ss_pred CCCceEEeccCceeeeecc-CCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceeecCCCC
Q 008947 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (548)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 293 (548)
-|+--|....+....|-|. |+...|..|-+- - .+..++.||.|+....+--||.
T Consensus 41 ICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEY-E------------------------RkeGnq~CPQCkTrYkR~Kgsp 95 (1085)
T PLN02400 41 ICGDDVGVTETGDVFVACNECAFPVCRPCYEY-E------------------------RKDGTQCCPQCKTRYRRHKGSP 95 (1085)
T ss_pred ecccccCcCCCCCEEEEEccCCCccccchhhe-e------------------------cccCCccCcccCCccccccCCC
Confidence 5777777666666789998 999999998631 0 0123378888888877666665
Q ss_pred ce
Q 008947 294 LV 295 (548)
Q Consensus 294 hM 295 (548)
.+
T Consensus 96 rV 97 (1085)
T PLN02400 96 RV 97 (1085)
T ss_pred CC
Confidence 44
No 281
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=22.55 E-value=76 Score=24.18 Aligned_cols=33 Identities=27% Similarity=0.440 Sum_probs=20.2
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCccccCcC
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCL 243 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~ 243 (548)
..|| +|++.-.+-+.....|.|. |+...|.-=+
T Consensus 8 VkCp---~C~~~q~vFSha~t~V~C~~Cg~~L~~PtG 41 (55)
T PF01667_consen 8 VKCP---GCYNIQTVFSHAQTVVKCVVCGTVLAQPTG 41 (55)
T ss_dssp EE-T---TT-SEEEEETT-SS-EE-SSSTSEEEEE-S
T ss_pred EECC---CCCCeeEEEecCCeEEEcccCCCEecCCCC
Confidence 4687 8998877666666679997 9999886433
No 282
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.48 E-value=31 Score=35.32 Aligned_cols=26 Identities=31% Similarity=0.863 Sum_probs=18.2
Q ss_pred CcCCCCCCcceeecCCCCceEe----ccccccccccccc
Q 008947 276 TKPCPKCHKPVEKNGGCNLVSC----ICGQAFCWLCGGA 310 (548)
Q Consensus 276 tK~CPkC~~~IEKn~GCnhMtC----~C~~~FCw~C~~~ 310 (548)
++.||-|.-. |.| .|+|.||++|.+.
T Consensus 7 ~~eC~IC~nt---------~n~Pv~l~C~HkFCyiCiKG 36 (324)
T KOG0824|consen 7 KKECLICYNT---------GNCPVNLYCFHKFCYICIKG 36 (324)
T ss_pred CCcceeeecc---------CCcCccccccchhhhhhhcc
Confidence 3678777532 334 2999999999865
No 283
>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=22.36 E-value=75 Score=24.53 Aligned_cols=26 Identities=35% Similarity=0.792 Sum_probs=18.3
Q ss_pred cCCCCCCcc----eeecCCCCceEe-ccccc
Q 008947 277 KPCPKCHKP----VEKNGGCNLVSC-ICGQA 302 (548)
Q Consensus 277 K~CPkC~~~----IEKn~GCnhMtC-~C~~~ 302 (548)
-.||+|+.. +-+..|=.++.| .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 379999864 224566688889 58875
No 284
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=22.22 E-value=38 Score=24.96 Aligned_cols=44 Identities=23% Similarity=0.484 Sum_probs=21.9
Q ss_pred cccccccccccccCceecCCC-CccchhhHHHHHHhhhccCCccceecCccccccccch
Q 008947 117 VMCDICMEEVAGDKATKMDCG-HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (548)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~Cg-H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~~ 174 (548)
+.|--|+-.. --.+.|. |+.|..|++..+.. .-.||. |...+|.
T Consensus 3 ~nCKsCWf~~----k~Li~C~dHYLCl~CLt~ml~~--------s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN----KGLIKCSDHYLCLNCLTLMLSR--------SDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S------SSEEE-SS-EEEHHHHHHT-SS--------SSEETT--TTEE---
T ss_pred ccChhhhhcC----CCeeeecchhHHHHHHHHHhcc--------ccCCCc--ccCcCcc
Confidence 4577776542 1223565 99999999988764 237888 8877664
No 285
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=22.10 E-value=50 Score=32.76 Aligned_cols=16 Identities=38% Similarity=0.885 Sum_probs=13.4
Q ss_pred cCCCccccCcCccCCC
Q 008947 233 ACGAQFCFSCLSEAHS 248 (548)
Q Consensus 233 ~Cg~~fC~~C~~~~H~ 248 (548)
.|++.||..|....|.
T Consensus 22 aC~HvfC~~C~k~~~~ 37 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSP 37 (233)
T ss_pred echhhhhhhhcccCCc
Confidence 4999999999887664
No 286
>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=21.96 E-value=30 Score=40.31 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=0.0
Q ss_pred cCCCCCCcceeec
Q 008947 277 KPCPKCHKPVEKN 289 (548)
Q Consensus 277 K~CPkC~~~IEKn 289 (548)
..||.|+..+...
T Consensus 681 ~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 681 YVCPDCGIEVEED 693 (900)
T ss_dssp -------------
T ss_pred eeccccccccCcc
Confidence 5788888777665
No 287
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=21.64 E-value=77 Score=28.52 Aligned_cols=20 Identities=50% Similarity=1.323 Sum_probs=11.0
Q ss_pred cCCCC--CCcceeecCCCCceEec--cccc
Q 008947 277 KPCPK--CHKPVEKNGGCNLVSCI--CGQA 302 (548)
Q Consensus 277 K~CPk--C~~~IEKn~GCnhMtC~--C~~~ 302 (548)
|.||+ |.-.++ +|-|+ ||+-
T Consensus 83 k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 83 KPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp SB-SS--S--BEE------EE---TBTTB-
T ss_pred CCCCccccCCcee------EEeccCcCCCc
Confidence 99999 998888 67884 8764
No 288
>cd07630 BAR_SNX_like The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of uncharacterized proteins with similarity to sorting nexins (SNXs), which are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.59 E-value=7.3e+02 Score=23.89 Aligned_cols=62 Identities=13% Similarity=0.276 Sum_probs=47.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008947 431 IKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 492 (548)
Q Consensus 431 ~~~~lfe~~Q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (548)
.++..-|..|+.++..-|.+|..+..++..+....+..+|.-++.++...-.+-++.++.+.
T Consensus 132 ~k~~~ae~~~~~a~~~fe~iS~~~k~EL~rF~~~Rv~~fk~~l~~~~E~~i~~ak~~~~~~~ 193 (198)
T cd07630 132 QKKEQAEEAKKKAETEFEEISSLAKKELERFHRQRVLELQSALVCYAESQIKNAKEAAAVLT 193 (198)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556788888899999999999998888777777788887777777776666666665554
No 289
>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=21.55 E-value=74 Score=22.51 Aligned_cols=26 Identities=38% Similarity=0.782 Sum_probs=13.6
Q ss_pred cCCCCCCCCceEEeccCceeeeecc-CCCc
Q 008947 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (548)
.|| .|+.-....+.....+.|+ ||..
T Consensus 2 ~Cp---~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCP---NCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBT---TTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCc---CCcCCceEEcCCCCeEECCCCCCE
Confidence 477 6887543333333345665 6654
No 290
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=21.28 E-value=51 Score=33.58 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=8.4
Q ss_pred CCCCCCCCCCcc
Q 008947 1 MEDSFSGDEDYY 12 (548)
Q Consensus 1 m~d~~~~~~~~~ 12 (548)
|.|.++||||||
T Consensus 1 m~D~~MdddEDY 12 (440)
T KOG1464|consen 1 MSDDFMDDDEDY 12 (440)
T ss_pred CCccccccchhc
Confidence 777777666666
No 291
>PRK00420 hypothetical protein; Validated
Probab=21.15 E-value=1.9e+02 Score=25.46 Aligned_cols=43 Identities=23% Similarity=0.329 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHHHhhhcCcccccCCCCCCCCceEEeccCceeeeeccCCCccccCcCc
Q 008947 187 NLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLS 244 (548)
Q Consensus 187 e~~~ky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~ 244 (548)
+...+..+.++..+..- -..|| .|+..+..... |..||..|+.
T Consensus 6 ~~~k~~a~~Ll~Ga~ml---~~~CP---~Cg~pLf~lk~---------g~~~Cp~Cg~ 48 (112)
T PRK00420 6 DIVKKAAELLLKGAKML---SKHCP---VCGLPLFELKD---------GEVVCPVHGK 48 (112)
T ss_pred HHHHHHHHHHHhHHHHc---cCCCC---CCCCcceecCC---------CceECCCCCC
Confidence 44445555555543332 25798 69977653211 4556666665
No 292
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.12 E-value=59 Score=31.06 Aligned_cols=23 Identities=35% Similarity=0.993 Sum_probs=15.0
Q ss_pred cCCCCCCcceeecCCCCceEe-cccc
Q 008947 277 KPCPKCHKPVEKNGGCNLVSC-ICGQ 301 (548)
Q Consensus 277 K~CPkC~~~IEKn~GCnhMtC-~C~~ 301 (548)
-.|++|+.++++ .=+.|+| +||.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 367777777777 2355677 4665
No 293
>PLN00209 ribosomal protein S27; Provisional
Probab=21.12 E-value=88 Score=26.02 Aligned_cols=34 Identities=24% Similarity=0.365 Sum_probs=25.7
Q ss_pred ccCCCCCCCCceEEeccCceeeeecc-CCCccccCcCc
Q 008947 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLS 244 (548)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~ 244 (548)
+.|| +|++.-.+-+.....|.|. ||...|.-=+.
T Consensus 37 VkCp---~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGG 71 (86)
T PLN00209 37 VKCQ---GCFNITTVFSHSQTVVVCGSCQTVLCQPTGG 71 (86)
T ss_pred EECC---CCCCeeEEEecCceEEEccccCCEeeccCCC
Confidence 5788 8998877666666779997 99998865443
No 294
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.12 E-value=1.8e+02 Score=25.34 Aligned_cols=34 Identities=24% Similarity=0.628 Sum_probs=18.9
Q ss_pred eeeecc-CCCc--cccCcCccCCCCCCchhhHHHHHh
Q 008947 228 CEVECA-CGAQ--FCFSCLSEAHSPCSCSMWDLWAKK 261 (548)
Q Consensus 228 ~~v~C~-Cg~~--fC~~C~~~~H~p~~C~~~~~w~~~ 261 (548)
....|+ ||+. ..++|+...=+-+.-....+|..+
T Consensus 41 ~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~~~~~W~~~ 77 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSCKNRHCPSCQAKATEQWIEK 77 (111)
T ss_pred ceeecCCCCceEEecCcccCcCCCCCCChHHHHHHHH
Confidence 346786 8876 577887652233333344455543
No 295
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=21.05 E-value=4.1e+02 Score=30.87 Aligned_cols=23 Identities=9% Similarity=0.044 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 008947 470 RMQVINLSVITDTLCKKMYECIE 492 (548)
Q Consensus 470 k~~~~~l~~~~~~~~~~l~~~~e 492 (548)
-.++.++.+.+.+++..+|+.++
T Consensus 312 ~~~i~s~~~k~~~~~~~I~ka~~ 334 (683)
T PF08580_consen 312 SKQIESKEKKKSHYFPAIYKARV 334 (683)
T ss_pred HHHHHHHHHHHhccHHHHHHHHH
Confidence 34444445444445444444433
No 296
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.97 E-value=65 Score=37.19 Aligned_cols=48 Identities=15% Similarity=0.357 Sum_probs=32.4
Q ss_pred ccccccccccccccCc-eecCCCCccchhhHHHHHHhhhccCCccceecCccccccccc
Q 008947 116 TVMCDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~i~ 173 (548)
.-.|++|+..+..... ....|+|.||..|+..|-... =.||. |...+.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~ 171 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFG 171 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhhh
Confidence 3568888877643222 234899999999999986542 26877 665543
No 297
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=20.87 E-value=67 Score=31.98 Aligned_cols=41 Identities=29% Similarity=0.835 Sum_probs=16.1
Q ss_pred HHHHHHhhhcCcccccCCCCCCCCce-EEe-c-cCceeeeecc-CCCcccc
Q 008947 194 RFLLESFIEDNKMVKWCPSTPHCGNA-IRV-E-EVEVCEVECA-CGAQFCF 240 (548)
Q Consensus 194 ~~l~~~~v~~~~~~~~CP~~p~C~~~-i~~-~-~~~~~~v~C~-Cg~~fC~ 240 (548)
+.+.+.+|..+ .+|| .||.. +.. . .....++.|+ |+..|=.
T Consensus 21 RVltE~Wv~~n---~yCP---~Cg~~~L~~f~NN~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 21 RVLTEDWVAEN---MYCP---NCGSKPLSKFENNRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp HHHHHHHHHHH------T---TT--SS-EE--------EEE-TTT--EEEE
T ss_pred HHHHHHHHHHC---CcCC---CCCChhHhhccCCCccceeECCCCchHHhh
Confidence 55666777654 3898 79987 432 2 2445567776 7666543
No 298
>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=20.83 E-value=47 Score=22.31 Aligned_cols=10 Identities=30% Similarity=1.006 Sum_probs=5.2
Q ss_pred cCCCCCCcce
Q 008947 277 KPCPKCHKPV 286 (548)
Q Consensus 277 K~CPkC~~~I 286 (548)
-+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 4666666544
No 299
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.76 E-value=48 Score=25.95 Aligned_cols=14 Identities=57% Similarity=1.054 Sum_probs=11.7
Q ss_pred CCcCCCCCCcceee
Q 008947 275 HTKPCPKCHKPVEK 288 (548)
Q Consensus 275 ~tK~CPkC~~~IEK 288 (548)
.+.+||.|+++++.
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 35799999999984
No 300
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.70 E-value=1.3e+02 Score=23.02 Aligned_cols=29 Identities=17% Similarity=0.360 Sum_probs=25.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChHH
Q 008947 54 DLRRVMELLSLREHHARTLLIHYRWDVEK 82 (548)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~ 82 (548)
.+.+|++.||++......-...++|+...
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~ 43 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELL 43 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccC
Confidence 46789999999999999999999998644
No 301
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.64 E-value=1.1e+02 Score=24.89 Aligned_cols=48 Identities=23% Similarity=0.609 Sum_probs=20.4
Q ss_pred cccccccccccccc---cCceec--CCCCccchhhHHHHHHhhhccCCccceecCccccccc
Q 008947 115 STVMCDICMEEVAG---DKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (548)
Q Consensus 115 ~~~~C~IC~e~~~~---~~~~~l--~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 171 (548)
....|.||-+++.. .++|.. .|+-..|+.|+.-- .++|. -.||. |+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE----rkeg~---q~Cpq--Ckt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE----RKEGN---QVCPQ--CKTR 60 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH----HHTS----SB-TT--T--B
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH----hhcCc---ccccc--cCCC
Confidence 34689999998643 344443 78899999998653 44554 46888 7753
No 302
>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=20.39 E-value=95 Score=28.92 Aligned_cols=36 Identities=28% Similarity=0.570 Sum_probs=23.1
Q ss_pred ccccccccccccccCceecC-------CCCccc------hhhHHHHHHhhh
Q 008947 116 TVMCDICMEEVAGDKATKMD-------CGHCFC------NDCWTEHFIVKI 153 (548)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~-------CgH~fC------~~C~~~yl~~~i 153 (548)
..+|+||++-- -+.+.|- |.-+.| .+|+.+|-....
T Consensus 2 d~~CpICme~P--HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEHP--HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccCC--CceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 46899999862 3555543 333444 578888876544
No 303
>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=20.35 E-value=52 Score=24.41 Aligned_cols=35 Identities=20% Similarity=0.523 Sum_probs=24.2
Q ss_pred cccccccccccccC--ceecCCCCccchhhHHHHHHh
Q 008947 117 VMCDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIV 151 (548)
Q Consensus 117 ~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~ 151 (548)
..|.+|-..|.... ..--.||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 36888877765321 122379999999999987554
No 304
>PHA02325 hypothetical protein
Probab=20.28 E-value=48 Score=25.89 Aligned_cols=11 Identities=55% Similarity=1.047 Sum_probs=7.4
Q ss_pred CCcCCCCCCcc
Q 008947 275 HTKPCPKCHKP 285 (548)
Q Consensus 275 ~tK~CPkC~~~ 285 (548)
++|.||+|++.
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 45778887654
No 305
>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=20.24 E-value=49 Score=27.22 Aligned_cols=28 Identities=36% Similarity=0.991 Sum_probs=11.7
Q ss_pred CcCCCCCCcc------eeecCCCCceEec-ccccc
Q 008947 276 TKPCPKCHKP------VEKNGGCNLVSCI-CGQAF 303 (548)
Q Consensus 276 tK~CPkC~~~------IEKn~GCnhMtC~-C~~~F 303 (548)
+=.||.|+.. |.|..|=-+++|+ ||..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 3589999822 2345555567773 65544
No 306
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=20.23 E-value=8.3e+02 Score=29.77 Aligned_cols=15 Identities=47% Similarity=1.232 Sum_probs=12.2
Q ss_pred CcCCCCCCcceeecC
Q 008947 276 TKPCPKCHKPVEKNG 290 (548)
Q Consensus 276 tK~CPkC~~~IEKn~ 290 (548)
.-.||+|+.|+|-..
T Consensus 796 ~~~~~~~~~~~~~~~ 810 (1006)
T PRK12775 796 VATCPKCHRPLEGDE 810 (1006)
T ss_pred CccCcccCCCCCCCc
Confidence 468999999999543
No 307
>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=20.19 E-value=57 Score=33.25 Aligned_cols=52 Identities=25% Similarity=0.632 Sum_probs=33.7
Q ss_pred cCCCCCCCCceEEeccCceeeeeccCCCccccCcCccCCCCCCchhhHHHHHhhhchHHHHHHHHhCCcCCCCCCcceee
Q 008947 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEK 288 (548)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEK 288 (548)
-|| .|..-....++-...+. +|++..|-+|.-. ....+.-.||.|.++.-|
T Consensus 2 ~Cp---~CKt~~Y~np~lk~~in-~C~H~lCEsCvd~-------------------------iF~~g~~~CpeC~~iLRk 52 (300)
T KOG3800|consen 2 ACP---KCKTDRYLNPDLKLMIN-ECGHRLCESCVDR-------------------------IFSLGPAQCPECMVILRK 52 (300)
T ss_pred CCc---ccccceecCccceeeec-cccchHHHHHHHH-------------------------HHhcCCCCCCcccchhhh
Confidence 476 67766665554444455 7999999998531 012344689988888764
Q ss_pred c
Q 008947 289 N 289 (548)
Q Consensus 289 n 289 (548)
+
T Consensus 53 ~ 53 (300)
T KOG3800|consen 53 N 53 (300)
T ss_pred c
Confidence 4
No 308
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.16 E-value=66 Score=24.63 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.4
Q ss_pred CCcCCCCCCccee
Q 008947 275 HTKPCPKCHKPVE 287 (548)
Q Consensus 275 ~tK~CPkC~~~IE 287 (548)
+.-.||+|+.+..
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 4468999998887
Done!