Query 011726
Match_columns 478
No_of_seqs 369 out of 1600
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 04:33:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011726.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011726hhsearch_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 4.6E-67 1E-71 543.5 25.7 410 40-477 1-417 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 6.1E-36 1.3E-40 302.5 10.1 223 115-363 145-374 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 2.1E-35 4.5E-40 286.3 12.9 203 115-322 183-415 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 2.6E-26 5.7E-31 215.0 8.4 196 113-317 218-441 (446)
5 smart00647 IBR In Between Ring 99.3 4.1E-12 8.8E-17 96.1 5.9 62 190-252 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 4.4E-12 9.6E-17 95.9 -0.1 62 190-252 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 1.4E-08 3E-13 69.6 1.2 41 119-165 1-41 (42)
8 PF13923 zf-C3HC4_2: Zinc fing 98.3 4.4E-07 9.6E-12 61.2 1.9 37 119-165 1-38 (39)
9 PF13639 zf-RING_2: Ring finge 98.3 4.9E-07 1.1E-11 62.7 2.1 40 118-165 2-42 (44)
10 PF00097 zf-C3HC4: Zinc finger 98.3 8.2E-07 1.8E-11 60.5 3.2 39 119-165 1-40 (41)
11 smart00647 IBR In Between Ring 98.2 1.5E-06 3.3E-11 65.3 4.4 38 275-312 17-59 (64)
12 PF01485 IBR: IBR domain; Int 98.2 7.7E-07 1.7E-11 66.9 2.0 38 275-312 17-59 (64)
13 KOG0320 Predicted E3 ubiquitin 98.1 1.5E-06 3.2E-11 76.8 2.6 52 114-175 129-180 (187)
14 PLN03208 E3 ubiquitin-protein 98.1 3.1E-06 6.7E-11 76.8 4.0 65 114-182 16-88 (193)
15 PF13445 zf-RING_UBOX: RING-ty 98.1 2.1E-06 4.5E-11 58.8 2.2 41 119-164 1-43 (43)
16 PF14634 zf-RING_5: zinc-RING 97.9 6.2E-06 1.4E-10 57.1 2.6 42 118-169 1-43 (44)
17 PF13920 zf-C3HC4_3: Zinc fing 97.9 9.8E-06 2.1E-10 57.8 3.1 46 116-173 2-48 (50)
18 cd00162 RING RING-finger (Real 97.9 1.2E-05 2.6E-10 55.3 3.5 44 118-171 1-44 (45)
19 smart00184 RING Ring finger. E 97.7 4E-05 8.6E-10 50.7 2.9 38 119-165 1-38 (39)
20 KOG0823 Predicted E3 ubiquitin 97.6 2.2E-05 4.7E-10 72.6 1.8 55 114-177 45-99 (230)
21 smart00504 Ubox Modified RING 97.6 6.1E-05 1.3E-09 56.3 3.9 48 117-176 2-49 (63)
22 PHA02926 zinc finger-like prot 97.6 4.1E-05 8.9E-10 70.3 3.0 55 114-172 168-229 (242)
23 KOG2164 Predicted E3 ubiquitin 97.6 3.2E-05 7E-10 79.1 2.2 59 116-181 186-244 (513)
24 PHA02929 N1R/p28-like protein; 97.5 7.5E-05 1.6E-09 70.8 3.4 48 115-172 173-226 (238)
25 KOG0317 Predicted E3 ubiquitin 97.4 7E-05 1.5E-09 71.4 1.8 50 115-176 238-287 (293)
26 TIGR00599 rad18 DNA repair pro 97.3 0.00015 3.2E-09 73.9 3.5 50 114-175 24-73 (397)
27 KOG2177 Predicted E3 ubiquitin 97.3 0.00012 2.5E-09 72.6 2.5 43 115-169 12-54 (386)
28 KOG4367 Predicted Zn-finger pr 97.2 0.0013 2.8E-08 65.7 8.2 34 115-150 3-36 (699)
29 KOG0287 Postreplication repair 97.2 0.00027 5.8E-09 68.5 3.3 63 115-193 22-86 (442)
30 PF11789 zf-Nse: Zinc-finger o 96.9 0.00061 1.3E-08 49.8 2.2 47 115-169 10-57 (57)
31 TIGR00570 cdk7 CDK-activating 96.9 0.00067 1.5E-08 66.3 2.9 53 117-178 4-59 (309)
32 KOG0978 E3 ubiquitin ligase in 96.8 0.00034 7.4E-09 75.2 0.5 55 115-180 642-696 (698)
33 COG5540 RING-finger-containing 96.6 0.0011 2.3E-08 63.6 2.4 52 114-174 321-373 (374)
34 PF14555 UBA_4: UBA-like domai 96.5 0.0083 1.8E-07 41.2 5.4 39 53-91 2-40 (43)
35 PF14835 zf-RING_6: zf-RING of 96.5 0.00046 9.9E-09 50.9 -1.0 46 116-175 7-53 (65)
36 KOG1002 Nucleotide excision re 96.4 0.0017 3.7E-08 66.5 2.2 55 114-175 534-588 (791)
37 KOG4628 Predicted E3 ubiquitin 96.3 0.0025 5.5E-08 63.4 2.6 45 117-170 230-275 (348)
38 PF04564 U-box: U-box domain; 96.1 0.0032 6.9E-08 48.7 1.8 50 115-175 3-52 (73)
39 COG5574 PEX10 RING-finger-cont 96.1 0.0052 1.1E-07 58.2 3.5 53 115-177 214-266 (271)
40 PF12678 zf-rbx1: RING-H2 zinc 96.0 0.0034 7.3E-08 48.5 1.5 41 117-165 20-71 (73)
41 KOG0804 Cytoplasmic Zn-finger 95.8 0.3 6.5E-06 49.8 14.5 117 41-170 85-219 (493)
42 PF11793 FANCL_C: FANCL C-term 95.4 0.0091 2E-07 45.7 1.7 57 116-174 2-67 (70)
43 KOG2879 Predicted E3 ubiquitin 94.9 0.024 5.2E-07 53.9 3.6 50 114-173 237-287 (298)
44 KOG1812 Predicted E3 ubiquitin 94.8 0.026 5.6E-07 58.0 3.8 41 205-249 304-344 (384)
45 KOG1814 Predicted E3 ubiquitin 94.8 0.14 3E-06 51.6 8.7 38 274-311 271-311 (445)
46 COG5432 RAD18 RING-finger-cont 94.8 0.013 2.7E-07 56.0 1.3 47 115-173 24-70 (391)
47 KOG0824 Predicted E3 ubiquitin 94.7 0.018 3.9E-07 55.5 2.1 54 114-178 5-58 (324)
48 KOG1039 Predicted E3 ubiquitin 94.4 0.038 8.2E-07 55.4 3.8 54 114-170 159-218 (344)
49 COG5243 HRD1 HRD ubiquitin lig 94.2 0.038 8.3E-07 54.6 3.1 48 115-172 286-344 (491)
50 PF14570 zf-RING_4: RING/Ubox 94.1 0.03 6.4E-07 39.1 1.6 44 119-171 1-46 (48)
51 PF10571 UPF0547: Uncharacteri 94.0 0.028 6.1E-07 34.0 1.2 23 277-303 1-24 (26)
52 KOG0826 Predicted E3 ubiquitin 93.4 0.4 8.6E-06 47.0 8.5 80 82-172 259-347 (357)
53 PRK00420 hypothetical protein; 93.4 0.63 1.4E-05 38.9 8.6 27 276-310 23-49 (112)
54 KOG1428 Inhibitor of type V ad 93.2 0.14 3E-06 58.7 5.5 75 115-195 3485-3562(3738)
55 KOG4159 Predicted E3 ubiquitin 93.1 0.13 2.8E-06 52.7 5.0 49 114-174 82-130 (398)
56 COG5152 Uncharacterized conser 93.1 0.032 7E-07 50.4 0.5 33 115-149 195-227 (259)
57 KOG4185 Predicted E3 ubiquitin 92.7 0.13 2.9E-06 50.9 4.4 55 117-180 4-64 (296)
58 KOG1645 RING-finger-containing 92.5 0.089 1.9E-06 52.8 2.7 49 116-172 4-55 (463)
59 KOG0311 Predicted E3 ubiquitin 92.0 0.028 6.1E-07 55.4 -1.4 47 115-171 42-88 (381)
60 KOG2817 Predicted E3 ubiquitin 92.0 0.73 1.6E-05 46.5 8.4 126 40-177 255-389 (394)
61 KOG0006 E3 ubiquitin-protein l 91.6 0.38 8.2E-06 46.8 5.7 94 135-250 341-439 (446)
62 KOG2660 Locus-specific chromos 91.2 0.15 3.2E-06 50.0 2.6 47 115-172 14-60 (331)
63 PF12861 zf-Apc11: Anaphase-pr 91.0 0.18 3.8E-06 39.8 2.4 31 135-172 51-81 (85)
64 KOG0802 E3 ubiquitin ligase [P 90.2 0.16 3.5E-06 54.9 2.1 44 116-167 291-337 (543)
65 COG5220 TFB3 Cdk activating ki 89.9 0.07 1.5E-06 49.7 -0.8 50 116-172 10-63 (314)
66 smart00744 RINGv The RING-vari 89.6 0.37 8E-06 34.0 2.8 42 118-165 1-47 (49)
67 PF05883 Baculo_RING: Baculovi 89.5 0.14 3.1E-06 43.9 0.8 34 116-149 26-66 (134)
68 KOG1734 Predicted RING-contain 89.5 0.16 3.4E-06 48.3 1.1 53 115-175 223-283 (328)
69 smart00661 RPOL9 RNA polymeras 89.2 0.31 6.7E-06 34.6 2.3 27 277-303 1-30 (52)
70 KOG4692 Predicted E3 ubiquitin 89.2 0.24 5.3E-06 48.8 2.2 51 112-174 418-468 (489)
71 KOG1785 Tyrosine kinase negati 89.0 0.16 3.4E-06 50.8 0.8 46 117-170 370-415 (563)
72 KOG0828 Predicted E3 ubiquitin 88.6 0.23 4.9E-06 51.1 1.7 51 114-173 569-634 (636)
73 TIGR00570 cdk7 CDK-activating 88.5 0.21 4.6E-06 49.1 1.4 53 209-290 5-57 (309)
74 PHA00626 hypothetical protein 88.5 0.29 6.3E-06 35.0 1.6 30 278-307 2-37 (59)
75 PF13240 zinc_ribbon_2: zinc-r 87.7 0.3 6.5E-06 28.6 1.1 11 278-288 1-11 (23)
76 KOG4265 Predicted E3 ubiquitin 87.5 0.59 1.3E-05 46.5 3.8 48 114-173 288-336 (349)
77 KOG4739 Uncharacterized protei 86.7 0.14 3.1E-06 48.1 -0.9 45 117-173 4-48 (233)
78 KOG1815 Predicted E3 ubiquitin 86.3 0.39 8.4E-06 50.5 1.9 38 276-313 158-198 (444)
79 PF14952 zf-tcix: Putative tre 86.1 0.5 1.1E-05 32.0 1.6 30 270-303 5-37 (44)
80 PF00627 UBA: UBA/TS-N domain; 85.9 2.9 6.3E-05 27.3 5.3 33 53-86 4-36 (37)
81 PRK00432 30S ribosomal protein 85.6 0.4 8.8E-06 34.0 1.1 27 275-303 19-47 (50)
82 PLN03086 PRLI-interacting fact 85.5 1.9 4.1E-05 46.3 6.5 57 159-238 406-463 (567)
83 PRK14559 putative protein seri 85.5 0.55 1.2E-05 51.4 2.6 24 277-311 28-51 (645)
84 COG4647 AcxC Acetone carboxyla 84.6 2.7 5.9E-05 35.5 5.7 110 172-287 17-131 (165)
85 PF13248 zf-ribbon_3: zinc-rib 84.1 0.62 1.4E-05 28.1 1.3 12 277-288 3-14 (26)
86 KOG1813 Predicted E3 ubiquitin 82.5 0.48 1E-05 45.9 0.5 44 116-171 241-284 (313)
87 PF09297 zf-NADH-PPase: NADH p 81.8 1.4 3E-05 27.9 2.3 28 275-302 2-30 (32)
88 KOG4445 Uncharacterized conser 81.3 3.8 8.3E-05 39.8 6.0 38 116-153 115-153 (368)
89 KOG1001 Helicase-like transcri 81.2 0.48 1E-05 52.2 -0.0 46 117-173 455-500 (674)
90 KOG3800 Predicted E3 ubiquitin 80.9 2 4.4E-05 41.6 4.0 48 118-174 2-52 (300)
91 PF02845 CUE: CUE domain; Int 80.8 6.5 0.00014 26.5 5.5 37 53-89 3-40 (42)
92 PF13719 zinc_ribbon_5: zinc-r 80.7 1.5 3.2E-05 28.9 2.2 28 208-238 3-35 (37)
93 KOG4172 Predicted E3 ubiquitin 80.6 0.56 1.2E-05 33.4 0.2 45 117-172 8-53 (62)
94 KOG0297 TNF receptor-associate 80.6 1.1 2.4E-05 46.2 2.4 43 113-165 18-61 (391)
95 KOG0317 Predicted E3 ubiquitin 80.5 0.26 5.7E-06 47.5 -2.0 35 272-312 235-270 (293)
96 PF13717 zinc_ribbon_4: zinc-r 80.4 1.6 3.4E-05 28.6 2.2 28 208-238 3-35 (36)
97 KOG3039 Uncharacterized conser 79.9 1.1 2.4E-05 42.2 1.8 53 115-177 220-274 (303)
98 PRK00398 rpoP DNA-directed RNA 79.7 1.3 2.8E-05 30.7 1.8 29 277-305 4-33 (46)
99 PF10367 Vps39_2: Vacuolar sor 79.6 0.68 1.5E-05 38.1 0.4 32 115-146 77-108 (109)
100 PF04641 Rtf2: Rtf2 RING-finge 79.2 1.6 3.4E-05 42.5 2.9 58 114-182 111-170 (260)
101 PF02150 RNA_POL_M_15KD: RNA p 79.2 1.4 3E-05 28.7 1.7 27 208-237 2-29 (35)
102 PF14835 zf-RING_6: zf-RING of 78.1 1.3 2.8E-05 33.0 1.4 34 277-310 8-49 (65)
103 TIGR00622 ssl1 transcription f 77.9 1.6 3.4E-05 36.4 2.0 38 208-248 56-101 (112)
104 KOG1701 Focal adhesion adaptor 77.8 1.1 2.3E-05 45.7 1.2 25 276-300 427-459 (468)
105 COG1998 RPS31 Ribosomal protei 77.4 1.8 3.9E-05 30.2 1.9 25 277-301 20-45 (51)
106 PF08274 PhnA_Zn_Ribbon: PhnA 77.3 1.6 3.5E-05 27.3 1.5 26 277-303 3-29 (30)
107 cd00194 UBA Ubiquitin Associat 77.2 8.7 0.00019 25.0 5.2 34 54-88 4-37 (38)
108 PF15227 zf-C3HC4_4: zinc fing 76.7 1.1 2.3E-05 30.5 0.6 29 279-312 1-29 (42)
109 KOG3002 Zn finger protein [Gen 76.5 4.3 9.3E-05 40.2 5.0 86 114-232 46-132 (299)
110 KOG1952 Transcription factor N 76.4 1.9 4.2E-05 47.5 2.8 50 115-165 190-241 (950)
111 KOG2807 RNA polymerase II tran 76.1 0.92 2E-05 44.5 0.2 84 138-248 276-365 (378)
112 COG5175 MOT2 Transcriptional r 75.4 1.3 2.7E-05 43.6 1.0 50 115-173 13-64 (480)
113 KOG2906 RNA polymerase III sub 75.4 1.5 3.3E-05 35.2 1.3 29 278-306 3-34 (105)
114 PRK14559 putative protein seri 75.1 2.1 4.5E-05 47.1 2.6 12 277-288 42-53 (645)
115 PHA03096 p28-like protein; Pro 74.7 1.7 3.7E-05 42.6 1.7 37 117-153 179-221 (284)
116 smart00165 UBA Ubiquitin assoc 74.2 9.2 0.0002 24.7 4.7 32 55-87 5-36 (37)
117 PRK04023 DNA polymerase II lar 73.9 2.3 4.9E-05 48.1 2.5 34 204-247 623-662 (1121)
118 KOG0320 Predicted E3 ubiquitin 73.4 0.96 2.1E-05 40.6 -0.3 29 233-287 150-178 (187)
119 PF09538 FYDLN_acid: Protein o 73.1 2.1 4.5E-05 35.7 1.6 26 277-303 10-36 (108)
120 KOG0827 Predicted E3 ubiquitin 72.5 1.2 2.6E-05 44.7 0.0 47 116-169 4-52 (465)
121 PF14447 Prok-RING_4: Prokaryo 72.5 1.6 3.5E-05 31.3 0.7 45 116-174 7-51 (55)
122 PF07282 OrfB_Zn_ribbon: Putat 70.7 3.3 7.3E-05 31.2 2.2 28 275-302 27-55 (69)
123 PF00643 zf-B_box: B-box zinc 70.6 3 6.6E-05 27.9 1.7 32 277-315 4-37 (42)
124 COG5222 Uncharacterized conser 70.5 2.7 5.8E-05 40.7 1.9 43 117-170 275-318 (427)
125 TIGR02098 MJ0042_CXXC MJ0042 f 70.5 4.4 9.6E-05 26.6 2.4 27 209-238 4-35 (38)
126 COG2888 Predicted Zn-ribbon RN 69.6 2.8 6.1E-05 30.5 1.4 6 278-283 29-34 (61)
127 PRK05654 acetyl-CoA carboxylas 69.3 1.3 2.8E-05 43.8 -0.5 28 276-303 27-56 (292)
128 KOG0978 E3 ubiquitin ligase in 69.3 1.9 4E-05 47.2 0.6 47 207-287 643-689 (698)
129 PRK14714 DNA polymerase II lar 68.3 4 8.8E-05 47.3 3.0 9 208-219 668-676 (1337)
130 smart00546 CUE Domain that may 66.7 22 0.00048 23.9 5.4 38 52-89 3-41 (43)
131 KOG1941 Acetylcholine receptor 66.7 2.5 5.5E-05 42.4 0.9 47 115-169 364-412 (518)
132 KOG3970 Predicted E3 ubiquitin 66.6 4.1 8.9E-05 37.9 2.2 55 116-172 50-104 (299)
133 PF14369 zf-RING_3: zinc-finge 66.2 4.8 0.0001 26.2 1.8 28 208-238 3-31 (35)
134 PRK08665 ribonucleotide-diphos 66.2 3.2 6.9E-05 46.6 1.7 26 277-304 725-751 (752)
135 PLN03208 E3 ubiquitin-protein 66.1 2 4.3E-05 39.5 0.1 32 276-312 18-49 (193)
136 KOG3579 Predicted E3 ubiquitin 65.3 7 0.00015 37.7 3.5 54 114-170 266-322 (352)
137 PF07191 zinc-ribbons_6: zinc- 64.9 4.2 9.1E-05 30.9 1.6 32 278-311 3-40 (70)
138 PF07975 C1_4: TFIIH C1-like d 64.1 2.7 5.9E-05 29.8 0.4 35 215-249 4-42 (51)
139 CHL00174 accD acetyl-CoA carbo 63.8 1.8 3.9E-05 42.6 -0.7 28 276-303 38-67 (296)
140 KOG0823 Predicted E3 ubiquitin 63.8 2 4.3E-05 40.3 -0.4 17 298-314 64-80 (230)
141 PRK00398 rpoP DNA-directed RNA 63.7 7.2 0.00016 26.9 2.5 28 209-240 5-33 (46)
142 TIGR03655 anti_R_Lar restricti 63.7 5.9 0.00013 28.3 2.1 11 277-287 2-12 (53)
143 PF06677 Auto_anti-p27: Sjogre 63.2 5.1 0.00011 27.1 1.6 22 277-300 18-41 (41)
144 cd00021 BBOX B-Box-type zinc f 63.2 5.9 0.00013 25.8 1.9 31 278-315 2-34 (39)
145 KOG1493 Anaphase-promoting com 63.1 1.5 3.2E-05 33.6 -1.1 48 118-172 22-80 (84)
146 PRK14714 DNA polymerase II lar 62.9 5 0.00011 46.6 2.4 10 277-286 668-677 (1337)
147 KOG2177 Predicted E3 ubiquitin 62.6 4.6 0.0001 39.3 2.0 16 293-308 96-112 (386)
148 PF13834 DUF4193: Domain of un 62.4 3.3 7.2E-05 33.5 0.7 33 112-144 66-98 (99)
149 TIGR00515 accD acetyl-CoA carb 61.9 2.1 4.5E-05 42.1 -0.7 29 276-304 26-56 (285)
150 KOG4275 Predicted E3 ubiquitin 61.7 3.2 6.9E-05 40.2 0.6 28 116-145 300-328 (350)
151 TIGR01384 TFS_arch transcripti 61.5 5.5 0.00012 32.7 1.9 24 277-302 1-25 (104)
152 PF12906 RINGv: RING-variant d 61.2 9.1 0.0002 26.6 2.7 33 119-151 1-38 (47)
153 COG1198 PriA Primosomal protei 61.2 5.8 0.00013 44.1 2.5 35 276-310 444-484 (730)
154 smart00661 RPOL9 RNA polymeras 61.1 6.4 0.00014 27.7 1.9 26 209-237 2-29 (52)
155 PF08938 HBS1_N: HBS1 N-termin 61.0 0.97 2.1E-05 35.4 -2.6 47 42-89 20-69 (79)
156 COG5219 Uncharacterized conser 60.4 5.4 0.00012 44.7 2.1 51 115-173 1468-1523(1525)
157 PF12773 DZR: Double zinc ribb 60.2 4.1 8.9E-05 28.5 0.8 12 277-288 30-41 (50)
158 TIGR00595 priA primosomal prot 60.0 6.9 0.00015 41.9 2.8 34 277-310 223-262 (505)
159 KOG2932 E3 ubiquitin ligase in 59.5 4.1 8.9E-05 39.8 0.9 53 204-292 87-139 (389)
160 COG1997 RPL43A Ribosomal prote 58.5 7.3 0.00016 30.8 1.9 28 276-303 35-63 (89)
161 COG1645 Uncharacterized Zn-fin 57.6 6.2 0.00013 33.9 1.5 24 276-308 28-51 (131)
162 PF01599 Ribosomal_S27: Riboso 57.2 6.6 0.00014 27.4 1.4 26 276-301 18-46 (47)
163 PF02318 FYVE_2: FYVE-type zin 56.6 20 0.00042 30.3 4.5 42 275-317 53-95 (118)
164 KOG3161 Predicted E3 ubiquitin 56.6 3.6 7.9E-05 44.0 -0.0 35 116-150 11-47 (861)
165 KOG2034 Vacuolar sorting prote 56.6 5.9 0.00013 44.2 1.6 38 115-152 816-853 (911)
166 COG0777 AccD Acetyl-CoA carbox 56.4 3.6 7.8E-05 39.7 -0.1 30 276-305 28-59 (294)
167 KOG0825 PHD Zn-finger protein 56.0 3.9 8.4E-05 44.8 0.1 41 115-155 95-140 (1134)
168 PF14803 Nudix_N_2: Nudix N-te 55.8 10 0.00022 24.5 2.0 27 208-237 1-31 (34)
169 PF05320 Pox_RNA_Pol_19: Poxvi 54.7 5.7 0.00012 34.7 0.9 10 115-124 125-134 (167)
170 TIGR00686 phnA alkylphosphonat 54.4 8.4 0.00018 31.8 1.8 26 277-303 3-29 (109)
171 KOG3268 Predicted E3 ubiquitin 54.1 14 0.00031 33.1 3.3 57 115-173 164-228 (234)
172 KOG3053 Uncharacterized conser 54.0 11 0.00023 36.0 2.6 53 115-170 19-79 (293)
173 COG5574 PEX10 RING-finger-cont 54.0 3.7 8E-05 39.3 -0.4 30 277-312 216-247 (271)
174 PF14445 Prok-RING_2: Prokaryo 53.9 2.5 5.5E-05 29.5 -1.1 34 115-148 6-40 (57)
175 PF03943 TAP_C: TAP C-terminal 52.3 20 0.00043 25.4 3.2 37 53-89 2-38 (51)
176 COG5151 SSL1 RNA polymerase II 52.2 3.5 7.6E-05 40.2 -0.8 89 137-248 307-408 (421)
177 PF14569 zf-UDP: Zinc-binding 52.0 7.1 0.00015 30.1 0.9 54 215-293 14-68 (80)
178 PF01363 FYVE: FYVE zinc finge 52.0 8.9 0.00019 28.8 1.5 37 113-149 6-44 (69)
179 COG5432 RAD18 RING-finger-cont 51.8 6 0.00013 38.3 0.6 32 277-315 26-59 (391)
180 PF03119 DNA_ligase_ZBD: NAD-d 51.6 12 0.00025 23.1 1.7 20 278-297 1-20 (28)
181 KOG1940 Zn-finger protein [Gen 51.5 13 0.00028 36.3 2.8 46 115-170 157-204 (276)
182 PF10446 DUF2457: Protein of u 51.2 11 0.00024 38.9 2.4 15 108-122 186-200 (458)
183 TIGR02300 FYDLN_acid conserved 51.0 9.2 0.0002 32.5 1.5 26 277-303 10-36 (129)
184 PRK14873 primosome assembly pr 50.9 11 0.00023 41.9 2.4 34 277-310 393-431 (665)
185 PRK09710 lar restriction allev 50.3 13 0.00028 27.7 2.0 14 275-288 5-18 (64)
186 KOG1571 Predicted E3 ubiquitin 50.2 8.1 0.00017 38.7 1.2 42 115-171 304-345 (355)
187 KOG0309 Conserved WD40 repeat- 49.9 13 0.00029 40.7 2.8 37 115-151 1027-1063(1081)
188 PF06827 zf-FPG_IleRS: Zinc fi 49.7 8.8 0.00019 23.7 1.0 24 277-300 2-28 (30)
189 PRK05580 primosome assembly pr 49.5 13 0.00027 41.6 2.8 34 277-310 391-430 (679)
190 KOG2114 Vacuolar assembly/sort 49.2 10 0.00022 42.1 1.9 40 117-170 841-880 (933)
191 smart00804 TAP_C C-terminal do 49.2 75 0.0016 23.6 6.0 41 49-89 10-50 (63)
192 PF14149 YhfH: YhfH-like prote 48.3 1.5 3.2E-05 28.8 -2.8 26 274-299 11-37 (37)
193 COG2051 RPS27A Ribosomal prote 48.0 20 0.00043 26.9 2.7 31 208-241 20-51 (67)
194 PF14446 Prok-RING_1: Prokaryo 47.7 15 0.00032 26.4 1.9 32 116-147 5-38 (54)
195 KOG3039 Uncharacterized conser 47.3 15 0.00033 34.8 2.5 37 117-155 44-80 (303)
196 KOG3130 Uncharacterized conser 47.3 11 0.00023 38.3 1.5 6 121-126 396-401 (514)
197 TIGR00993 3a0901s04IAP86 chlor 47.1 26 0.00056 38.7 4.5 41 38-82 412-452 (763)
198 PRK14892 putative transcriptio 47.0 13 0.00028 30.4 1.8 27 276-302 21-51 (99)
199 COG1594 RPB9 DNA-directed RNA 46.9 13 0.00027 31.3 1.8 27 277-303 3-32 (113)
200 PF06844 DUF1244: Protein of u 46.7 15 0.00033 27.4 1.9 18 139-156 11-28 (68)
201 PF05290 Baculo_IE-1: Baculovi 46.5 16 0.00035 31.4 2.3 51 115-172 79-131 (140)
202 PF06906 DUF1272: Protein of u 45.8 14 0.00031 26.6 1.6 44 117-172 6-51 (57)
203 PF10446 DUF2457: Protein of u 45.6 12 0.00025 38.7 1.6 6 346-351 407-412 (458)
204 PF03884 DUF329: Domain of unk 45.4 4.7 0.0001 29.4 -0.9 16 276-291 2-17 (57)
205 PRK04023 DNA polymerase II lar 45.0 15 0.00033 41.9 2.4 31 274-310 624-660 (1121)
206 TIGR00373 conserved hypothetic 44.9 30 0.00065 30.9 4.0 32 203-237 105-137 (158)
207 PF02891 zf-MIZ: MIZ/SP-RING z 44.5 25 0.00054 24.8 2.7 47 117-170 3-49 (50)
208 KOG2906 RNA polymerase III sub 44.5 23 0.0005 28.7 2.7 28 208-238 2-31 (105)
209 PRK10220 hypothetical protein; 44.5 15 0.00034 30.3 1.8 26 277-303 4-30 (111)
210 PF14471 DUF4428: Domain of un 43.4 17 0.00037 25.8 1.7 30 118-148 1-30 (51)
211 PRK12495 hypothetical protein; 43.2 29 0.00063 32.5 3.6 27 275-310 41-67 (226)
212 PRK14811 formamidopyrimidine-D 42.8 15 0.00033 35.8 1.9 22 276-297 235-258 (269)
213 COG0266 Nei Formamidopyrimidin 42.6 15 0.00032 35.8 1.8 25 276-300 245-272 (273)
214 PF10168 Nup88: Nuclear pore c 42.5 4.6E+02 0.0099 29.6 13.5 30 433-462 602-631 (717)
215 PF10122 Mu-like_Com: Mu-like 42.5 11 0.00024 26.6 0.6 25 277-301 5-32 (51)
216 KOG4196 bZIP transcription fac 42.4 54 0.0012 28.0 4.8 52 392-456 47-99 (135)
217 smart00336 BBOX B-Box-type zin 42.3 23 0.00049 23.3 2.2 32 277-315 4-37 (42)
218 PHA02929 N1R/p28-like protein; 42.1 11 0.00024 36.0 0.8 38 276-313 174-214 (238)
219 PRK11827 hypothetical protein; 41.7 20 0.00044 26.4 1.9 25 277-301 9-34 (60)
220 COG5236 Uncharacterized conser 41.5 16 0.00035 36.3 1.8 47 114-170 59-105 (493)
221 PF08792 A2L_zn_ribbon: A2L zi 40.6 23 0.0005 22.7 1.8 12 276-287 3-14 (33)
222 PF14569 zf-UDP: Zinc-binding 40.4 41 0.00088 26.1 3.4 48 115-171 8-60 (80)
223 PF13453 zf-TFIIB: Transcripti 40.3 17 0.00036 24.4 1.2 29 278-311 1-29 (41)
224 PRK01103 formamidopyrimidine/5 40.2 17 0.00038 35.5 1.9 25 276-300 245-272 (274)
225 COG3813 Uncharacterized protei 40.0 16 0.00036 27.6 1.2 44 117-172 6-51 (84)
226 TIGR00577 fpg formamidopyrimid 39.8 18 0.00039 35.4 1.9 25 276-300 245-272 (272)
227 PRK06266 transcription initiat 39.4 40 0.00086 30.7 4.0 20 54-73 38-57 (178)
228 smart00531 TFIIE Transcription 39.3 43 0.00092 29.4 4.0 19 56-74 19-37 (147)
229 PRK14810 formamidopyrimidine-D 39.2 18 0.00039 35.4 1.8 25 276-300 244-271 (272)
230 PF08746 zf-RING-like: RING-li 39.2 17 0.00036 24.8 1.1 41 119-165 1-42 (43)
231 PRK13945 formamidopyrimidine-D 38.9 19 0.00041 35.5 1.9 25 276-300 254-281 (282)
232 TIGR01206 lysW lysine biosynth 38.9 30 0.00065 24.9 2.4 27 209-238 4-32 (54)
233 PRK10445 endonuclease VIII; Pr 38.6 19 0.00041 35.1 1.8 25 276-300 235-262 (263)
234 PF04931 DNA_pol_phi: DNA poly 38.3 65 0.0014 36.6 6.3 20 68-87 764-783 (784)
235 KOG2164 Predicted E3 ubiquitin 38.1 12 0.00027 39.2 0.4 28 276-310 186-215 (513)
236 PF06044 DRP: Dam-replacing fa 37.8 21 0.00046 33.9 1.9 21 267-288 23-44 (254)
237 PF09723 Zn-ribbon_8: Zinc rib 36.8 34 0.00075 23.0 2.4 12 277-288 27-39 (42)
238 PF12959 DUF3848: Protein of u 36.7 1.5E+02 0.0033 24.2 6.3 47 42-89 24-75 (101)
239 KOG0825 PHD Zn-finger protein 36.5 26 0.00056 38.7 2.5 47 116-172 123-170 (1134)
240 PF04931 DNA_pol_phi: DNA poly 36.4 33 0.00072 39.0 3.6 9 57-65 707-715 (784)
241 smart00659 RPOLCX RNA polymera 36.1 26 0.00057 24.0 1.7 10 277-286 20-29 (44)
242 PF00098 zf-CCHC: Zinc knuckle 36.1 24 0.00052 19.2 1.2 16 238-253 2-17 (18)
243 COG5109 Uncharacterized conser 35.7 32 0.00069 33.9 2.8 51 115-172 335-386 (396)
244 PF07800 DUF1644: Protein of u 35.6 40 0.00086 30.0 3.1 37 116-154 2-51 (162)
245 PF06056 Terminase_5: Putative 35.1 53 0.0011 23.9 3.3 30 54-83 15-44 (58)
246 PF12861 zf-Apc11: Anaphase-pr 34.8 14 0.00031 29.2 0.2 35 277-314 33-67 (85)
247 PRK00415 rps27e 30S ribosomal 34.8 39 0.00086 24.8 2.5 31 208-241 12-43 (59)
248 PLN02189 cellulose synthase 34.1 28 0.00061 40.0 2.5 59 209-295 36-95 (1040)
249 TIGR02159 PA_CoA_Oxy4 phenylac 33.9 20 0.00044 31.5 1.1 95 48-148 41-140 (146)
250 COG2816 NPY1 NTP pyrophosphohy 33.7 41 0.00088 32.9 3.2 34 269-303 105-139 (279)
251 PRK08115 ribonucleotide-diphos 33.7 19 0.00041 40.8 1.0 24 277-302 828-853 (858)
252 PRK09521 exosome complex RNA-b 33.5 26 0.00055 32.2 1.8 25 278-303 151-176 (189)
253 PF05605 zf-Di19: Drought indu 33.4 67 0.0014 22.8 3.6 46 116-178 2-47 (54)
254 KOG0943 Predicted ubiquitin-pr 33.2 25 0.00054 40.8 1.8 20 435-454 2418-2437(3015)
255 PF03604 DNA_RNApol_7kD: DNA d 32.7 22 0.00047 22.6 0.8 10 277-286 18-27 (32)
256 COG5175 MOT2 Transcriptional r 32.5 11 0.00024 37.2 -0.8 30 209-243 16-45 (480)
257 PF07754 DUF1610: Domain of un 32.2 38 0.00082 20.1 1.7 7 277-283 17-23 (24)
258 PF05715 zf-piccolo: Piccolo Z 31.7 18 0.00038 26.4 0.3 34 277-310 3-39 (61)
259 PRK12286 rpmF 50S ribosomal pr 31.6 32 0.00069 25.1 1.6 13 275-287 26-38 (57)
260 COG3024 Uncharacterized protei 31.4 24 0.00052 26.2 0.9 14 275-288 6-19 (65)
261 PF08271 TF_Zn_Ribbon: TFIIB z 31.2 44 0.00096 22.5 2.2 26 209-237 2-28 (43)
262 PF14319 Zn_Tnp_IS91: Transpos 31.1 79 0.0017 26.4 4.2 37 207-262 42-78 (111)
263 PHA02926 zinc finger-like prot 30.9 21 0.00045 33.6 0.7 38 276-314 170-212 (242)
264 COG3809 Uncharacterized protei 30.9 30 0.00065 26.8 1.4 29 277-312 2-32 (88)
265 TIGR02443 conserved hypothetic 30.6 39 0.00083 24.8 1.9 27 277-303 10-41 (59)
266 PF14353 CpXC: CpXC protein 30.5 43 0.00092 28.5 2.5 11 209-222 3-13 (128)
267 PF14353 CpXC: CpXC protein 30.4 21 0.00045 30.5 0.6 50 161-223 2-51 (128)
268 KOG0824 Predicted E3 ubiquitin 30.2 18 0.00038 35.5 0.1 26 276-310 7-36 (324)
269 PF01667 Ribosomal_S27e: Ribos 30.1 47 0.001 24.0 2.2 33 208-243 8-41 (55)
270 PF14319 Zn_Tnp_IS91: Transpos 30.0 27 0.00058 29.2 1.2 8 277-284 61-68 (111)
271 smart00064 FYVE Protein presen 29.8 37 0.00081 25.2 1.8 36 116-151 10-47 (68)
272 cd00065 FYVE FYVE domain; Zinc 29.7 30 0.00065 24.6 1.2 35 117-151 3-39 (57)
273 COG2824 PhnA Uncharacterized Z 29.7 32 0.0007 28.3 1.5 25 277-303 4-30 (112)
274 COG1096 Predicted RNA-binding 29.4 30 0.00066 31.6 1.4 24 277-302 150-174 (188)
275 PF01428 zf-AN1: AN1-like Zinc 29.3 27 0.00058 23.7 0.8 26 214-245 4-30 (43)
276 TIGR01031 rpmF_bact ribosomal 28.9 32 0.00069 24.9 1.2 13 275-287 25-37 (55)
277 PHA02325 hypothetical protein 28.7 26 0.00057 25.9 0.7 11 275-285 2-12 (72)
278 KOG3800 Predicted E3 ubiquitin 28.0 36 0.00078 33.2 1.8 31 209-243 2-32 (300)
279 KOG4739 Uncharacterized protei 27.9 38 0.00083 32.1 1.9 16 233-248 22-37 (233)
280 PLN00209 ribosomal protein S27 27.7 57 0.0012 25.8 2.5 34 208-244 37-71 (86)
281 PHA02825 LAP/PHD finger-like p 27.7 54 0.0012 29.2 2.7 49 115-172 7-58 (162)
282 PTZ00083 40S ribosomal protein 27.5 57 0.0012 25.7 2.5 35 208-245 36-71 (85)
283 PLN02638 cellulose synthase A 27.0 42 0.00091 38.9 2.3 56 215-295 22-78 (1079)
284 PF01783 Ribosomal_L32p: Ribos 26.9 24 0.00053 25.5 0.3 13 275-287 25-37 (56)
285 PF06972 DUF1296: Protein of u 26.9 2.1E+02 0.0046 21.0 5.1 41 50-90 4-45 (60)
286 PRK06369 nac nascent polypepti 26.6 1.6E+02 0.0036 24.7 5.2 36 52-87 77-112 (115)
287 TIGR00264 alpha-NAC-related pr 26.4 1.7E+02 0.0037 24.7 5.2 33 52-84 79-111 (116)
288 PF03615 GCM: GCM motif protei 26.3 51 0.0011 28.3 2.2 21 277-303 83-107 (143)
289 PF03833 PolC_DP2: DNA polymer 26.2 22 0.00048 39.8 0.0 48 201-286 649-702 (900)
290 PF08882 Acetone_carb_G: Aceto 26.1 31 0.00067 28.7 0.8 12 294-305 24-35 (112)
291 PRK13130 H/ACA RNA-protein com 26.1 39 0.00083 24.6 1.2 29 275-316 4-32 (56)
292 PRK00420 hypothetical protein; 25.8 1.4E+02 0.0029 25.1 4.6 43 187-244 6-48 (112)
293 PF09889 DUF2116: Uncharacteri 25.6 35 0.00076 25.1 1.0 23 277-310 4-27 (59)
294 PF05129 Elf1: Transcription e 25.4 31 0.00067 27.1 0.7 28 276-303 22-56 (81)
295 KOG0801 Predicted E3 ubiquitin 25.3 25 0.00054 31.1 0.1 28 114-141 175-203 (205)
296 PF07503 zf-HYPF: HypF finger; 25.1 29 0.00063 22.6 0.4 30 140-171 1-30 (35)
297 KOG4362 Transcriptional regula 24.8 24 0.00052 38.7 -0.1 49 115-172 20-68 (684)
298 PRK00241 nudC NADH pyrophospha 24.7 52 0.0011 31.9 2.2 28 275-302 98-126 (256)
299 KOG0943 Predicted ubiquitin-pr 24.6 42 0.00092 39.1 1.8 17 279-295 2281-2297(3015)
300 KOG2932 E3 ubiquitin ligase in 24.3 33 0.00071 33.8 0.7 28 276-310 90-120 (389)
301 PF07295 DUF1451: Protein of u 24.0 40 0.00086 29.7 1.2 35 42-76 11-45 (146)
302 COG1645 Uncharacterized Zn-fin 24.0 49 0.0011 28.5 1.7 23 208-236 29-52 (131)
303 PLN02436 cellulose synthase A 24.0 55 0.0012 37.9 2.6 56 215-295 41-97 (1094)
304 KOG2979 Protein involved in DN 23.5 37 0.00081 32.6 1.0 47 117-170 177-223 (262)
305 COG1594 RPB9 DNA-directed RNA 23.3 72 0.0016 26.7 2.5 29 207-238 2-32 (113)
306 PLN03086 PRLI-interacting fact 23.1 42 0.00091 36.3 1.4 29 275-303 432-463 (567)
307 COG4640 Predicted membrane pro 23.0 43 0.00093 34.1 1.3 8 277-284 2-9 (465)
308 KOG2807 RNA polymerase II tran 22.6 49 0.0011 32.9 1.6 35 118-153 332-367 (378)
309 PLN02436 cellulose synthase A 22.3 71 0.0015 37.1 3.0 48 115-171 35-87 (1094)
310 PF04216 FdhE: Protein involve 22.3 36 0.00079 33.5 0.7 34 277-310 173-220 (290)
311 PF12760 Zn_Tnp_IS1595: Transp 22.2 1.6E+02 0.0035 20.1 3.7 26 276-301 18-45 (46)
312 KOG3540 Beta amyloid precursor 22.1 2.4E+02 0.0053 29.7 6.4 41 47-87 258-305 (615)
313 COG5194 APC11 Component of SCF 21.9 53 0.0012 25.6 1.3 17 135-151 53-69 (88)
314 COG3492 Uncharacterized protei 21.8 50 0.0011 26.3 1.2 17 139-155 42-58 (104)
315 smart00834 CxxC_CXXC_SSSS Puta 21.7 50 0.0011 21.6 1.1 13 277-289 27-39 (41)
316 KOG3970 Predicted E3 ubiquitin 21.2 38 0.00082 31.7 0.5 80 236-329 21-101 (299)
317 PLN02915 cellulose synthase A 21.1 66 0.0014 37.2 2.4 55 215-294 20-75 (1044)
318 PF09526 DUF2387: Probable met 21.1 70 0.0015 24.4 1.9 26 277-302 9-39 (71)
319 PF11781 RRN7: RNA polymerase 20.9 61 0.0013 21.2 1.3 30 271-302 3-34 (36)
320 PLN02189 cellulose synthase 20.9 70 0.0015 37.0 2.6 48 115-171 33-85 (1040)
321 PF09151 DUF1936: Domain of un 20.8 51 0.0011 20.6 0.8 11 277-287 2-12 (36)
322 PF09788 Tmemb_55A: Transmembr 20.8 87 0.0019 30.1 2.8 16 208-224 124-139 (256)
323 PF15616 TerY-C: TerY-C metal 20.8 67 0.0014 27.7 1.9 35 275-309 76-113 (131)
324 PF15616 TerY-C: TerY-C metal 20.5 60 0.0013 28.0 1.5 23 209-241 79-101 (131)
325 PF10426 zf-RAG1: Recombinatio 20.2 54 0.0012 20.5 0.8 23 160-182 2-24 (30)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.6e-67 Score=543.46 Aligned_cols=410 Identities=41% Similarity=0.797 Sum_probs=361.7
Q ss_pred eeeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhcCCCccCCCCCCCCccccccc
Q 011726 40 KVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPMLPLSSTVMC 119 (478)
Q Consensus 40 ~vl~~~~i~~~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~C 119 (478)
.|||++++...|.++|..|+++|+++..+|++||.+|.|+.+++++.|++ +.+.++..+|+.... .......|
T Consensus 1 ~vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~------~~~~~~~c 73 (444)
T KOG1815|consen 1 EVLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWP------KKKGDVQC 73 (444)
T ss_pred CCCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccC------CCCccccC
Confidence 37899999999999999999999999999999999999999999999996 567788888876543 22356899
Q ss_pred cccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCc-hHHHHHHHHHHH
Q 011726 120 DICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHP-NLAEKFERFLLE 198 (478)
Q Consensus 120 ~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~-e~~~~y~~~~~~ 198 (478)
.||++.++. .+..+.|||.||..||..|+..+|.+|....|+||..+|...+....|..+++ + +...+|.+++++
T Consensus 74 ~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s---~~~~~~ky~~~i~~ 149 (444)
T KOG1815|consen 74 GICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVS---DKEDKEKYQRYILR 149 (444)
T ss_pred CcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecC---CHHHHHHHHHHHHH
Confidence 999999865 67788999999999999999999998875459999999999999999999998 5 589999999999
Q ss_pred HHHhhCCCcccCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcC
Q 011726 199 SFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKP 278 (478)
Q Consensus 199 ~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~ 278 (478)
+||+.+..++|||+ |+|++++.........|.|.||+.|||.|+.+||.|.+|..+..|.++..+++++.+||..|+++
T Consensus 150 syve~~~~lkwCP~-~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~ 228 (444)
T KOG1815|consen 150 SYVEDNVPLKWCPA-PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKE 228 (444)
T ss_pred HHHhcCCccccCCC-CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCcc
Confidence 99999999999995 99999999755555679999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccccCCCCceEec---cccceeccccccccCCCCccccCCCcCCCCchhhhhH-HHHHHHHHhhHHHHHHHHh
Q 011726 279 CPKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKK-TERAKRELYRYMHYHNRYK 354 (478)
Q Consensus 279 CP~C~~~IeK~~GCnhm~C~---C~~~FCw~C~~~~~~~H~~~~~~~~~C~~~~~~~~~~-~~~~~~~l~ry~~y~~r~~ 354 (478)
||+|.++|||++|||||+|. |+++|||+|++.|. +|+.++ ++.||+|....... +..++..+.||.|||.||+
T Consensus 229 CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~-~h~~~~--~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~ 305 (444)
T KOG1815|consen 229 CPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS-DHGSST--GYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWM 305 (444)
T ss_pred CCCcccchhccCCccccccccCCcCCeeceeeecccc-cccccc--eeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHH
Confidence 99999999999999999993 99999999999985 454433 79999998877655 7788889999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHH-HHHh-hhhhccccchhHHHHHHHHHHHhhhhhhccceeeeeccCccccccccChHHHHHH
Q 011726 355 AHTDSFKLESKLKETVLEK-VSIS-EERESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIK 432 (478)
Q Consensus 355 ~h~~s~~~~~~l~~~i~~k-~~~~-~~~~~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~ 432 (478)
+|..+++++..+...+... ...+ ......+.+++|+.+|+.+|+++|++|+|||+|+||+..+ .+
T Consensus 306 ~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~~-------------~~ 372 (444)
T KOG1815|consen 306 EHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSEN-------------NK 372 (444)
T ss_pred hhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhccc-------------ch
Confidence 9999999998766665433 2222 2223457799999999999999999999999999999832 34
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCCchHHHHHHHHHhhcc
Q 011726 433 QHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLS 477 (478)
Q Consensus 433 ~~~fe~~q~~le~~~e~L~~~le~~~~~~~~~~~~~~k~~~~~l~ 477 (478)
+++||++|.+|+..+|.|+..++.++.+.+.+++..+|+++.++|
T Consensus 373 ~~~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~ 417 (444)
T KOG1815|consen 373 RNLFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLT 417 (444)
T ss_pred hhhhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccc
Confidence 589999999999999999999999888777888999999998886
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.1e-36 Score=302.49 Aligned_cols=223 Identities=32% Similarity=0.680 Sum_probs=183.5
Q ss_pred cccccccccccccc-CCcee-cCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCchHHHHH
Q 011726 115 STVMCDICMEEVAG-DKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKF 192 (478)
Q Consensus 115 ~~~~C~IC~e~~~~-~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y 192 (478)
...+|.||+.+.+. ..++. ..|+|.||.+||++|+..+..+| ..++||..+|+..++.+....+|+ +.+.++|
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt---~kl~e~~ 219 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLT---PKLREMW 219 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcC---HHHHHHH
Confidence 45789999955433 34554 58999999999999999984444 589999999999999999999999 8999999
Q ss_pred HHHHHHHHHhhCCCcccCCCCCCCCceEEecc----ccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHH
Q 011726 193 ERFLLESFIEDNKMVKWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESE 267 (478)
Q Consensus 193 ~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~----~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~ 267 (478)
.+++.+.++.....+ +|| .|+|...+.... .......|+ |+..||..|+.+||++.+|..+++|......++.
T Consensus 220 e~~~~e~~i~~~~~~-ycp-~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~ 297 (384)
T KOG1812|consen 220 EQRLKEEVIPSLDRV-YCP-YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDI 297 (384)
T ss_pred HHHHHHHhhhhhhcc-cCC-CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHH
Confidence 999999999988888 999 699988776433 223335676 9999999999999999999999999987777888
Q ss_pred HHHHHHhCCcCCCCCCCCccccCCCCceEeccccceeccccccccCCCCccccCCCcCCCCchhhhhHHHHHHHHHhhHH
Q 011726 268 TVNWITVHTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKKTERAKRELYRYM 347 (478)
Q Consensus 268 ~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~H~~~~~~~~~C~~~~~~~~~~~~~~~~~l~ry~ 347 (478)
+++++..+|++||+|+..|++++|||||+|+||++|||.|+++|..+. +.-+.|.++... .
T Consensus 298 ~~~~la~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~----~~~~~~~r~~~~---------------~ 358 (384)
T KOG1812|consen 298 TLKYLAKRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHN----GECYECCRYKES---------------T 358 (384)
T ss_pred HHHHHHHhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCC----ccccCccccccc---------------c
Confidence 899999999999999999999999999999999999999999974211 112456666543 6
Q ss_pred HHHHHHhhhhHHHHHH
Q 011726 348 HYHNRYKAHTDSFKLE 363 (478)
Q Consensus 348 ~y~~r~~~h~~s~~~~ 363 (478)
+++.++.+|.....++
T Consensus 359 ~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 359 HYFEDDENHDKSIQLE 374 (384)
T ss_pred cccccccccccccccc
Confidence 7777777666655443
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-35 Score=286.26 Aligned_cols=203 Identities=27% Similarity=0.666 Sum_probs=173.7
Q ss_pred cccccccccccccc-CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCchHHHHHH
Q 011726 115 STVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFE 193 (478)
Q Consensus 115 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~ 193 (478)
..+.|.|||++... ..+..++|+|+||+.|++.|++..|++|.+..++||.++|+...++..++.++. .++++||+
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 56899999999766 566778999999999999999999999999999999999999999999999999 99999999
Q ss_pred HHHHHHHHhhCCCcccCCCCCCCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchh--------HHHHH----
Q 011726 194 RFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMW--------DLWAK---- 260 (478)
Q Consensus 194 ~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~--------~~~~~---- 260 (478)
++++++.++...++++|| ++.|+.++..+++ ...+.|+ |..+||+.|+..||...+|..- ..|..
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-RACCQLPVKQDPG-RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCC-hhhccCccccCch-hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 999999999999999999 6899998854443 3458997 9999999999999999999743 12221
Q ss_pred ---------------HhhhhHHHHHHHHhCCcCCCCCCCCccccCCCCceEe-ccccceeccccccccCCCCccccCC
Q 011726 261 ---------------KCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTWSRIAG 322 (478)
Q Consensus 261 ---------------~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~~~~~~~ 322 (478)
...++-.+..|+..|.|+||+|+++|||++|||||+| .|++.|||+|+....+..+|+|..+
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 6999999999988766655665544
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=2.6e-26 Score=215.01 Aligned_cols=196 Identities=29% Similarity=0.630 Sum_probs=148.0
Q ss_pred ccccccccccccccccCCceecCCC--CccchhhHHHHHHHHHhcCCc-------ccccCCCcccCCccCHH-HHHHHhc
Q 011726 113 LSSTVMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQS-------KRIRCMAHKCNAICDEA-VVRNLVS 182 (478)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yi~~~i~~g~~-------~~i~CP~~~C~~~~~~~-~i~~ll~ 182 (478)
+....+|..|-+.- +.+..++|. |..|.+|++.|....+++.++ ..+.||. +|...+-.+ .--++|.
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 45678999998763 344556888 999999999999999987653 3456765 576644332 2235677
Q ss_pred CCCchHHHHHHHHHHHHHHhhCCCcccCCCCCCCCceEEeccccceeeEec--CCccccccccCCCCCCC----------
Q 011726 183 KKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA--CGAQFCFSCLSEAHSPC---------- 250 (478)
Q Consensus 183 ~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--C~~~fC~~C~~~~H~~~---------- 250 (478)
.+.+.+|+++..+.+|.....+ -|| +|+||..+.++++. ..|+|. ||..||..|...+|.+-
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 8999999999999999887755 899 69999998877744 358995 99999999999999751
Q ss_pred -Ccchh--HHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCCceEe-c--cccceeccccccccCCCCc
Q 011726 251 -SCSMW--DLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-I--CGQAFCWLCGGATGRDHTW 317 (478)
Q Consensus 251 -~C~~~--~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~--C~~~FCw~C~~~~~~~H~~ 317 (478)
+|... ..-.....-+..+..-|+..||+||+|+++.||||||+||.| + ||.+|||.|+-.|.+.-.|
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~Cmg 441 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMG 441 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhcc
Confidence 24310 000011112334445578889999999999999999999999 4 9999999999999765443
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.30 E-value=4.1e-12 Score=96.07 Aligned_cols=62 Identities=53% Similarity=1.095 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHhhCCCcccCCCCCCCCceEEec-cccceeeEec-CCccccccccCCCCCCCCc
Q 011726 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE-EVEVCEVECA-CGAQFCFSCLSEAHSPCSC 252 (478)
Q Consensus 190 ~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C 252 (478)
++|++++++++|+.++.++||| +|+|+.++... +.....|.|+ |+..||+.|+.+||.|.+|
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 69999999887 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=99.16 E-value=4.4e-12 Score=95.85 Aligned_cols=62 Identities=35% Similarity=0.960 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhhCCCcccCCCCCCCCceEEeccccce-eeEec-CCccccccccCCCCCCCCc
Q 011726 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVC-EVECA-CGAQFCFSCLSEAHSPCSC 252 (478)
Q Consensus 190 ~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-C~~~fC~~C~~~~H~~~~C 252 (478)
++|++++++.+++.++.++||| +|+|+.++...+.... .++|+ |++.||+.|+.+||.|.+|
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 4788899999998888999999 6999999997775444 38998 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=98.60 E-value=1.4e-08 Score=69.57 Aligned_cols=41 Identities=27% Similarity=0.797 Sum_probs=29.8
Q ss_pred ccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
|+||++.+ .++++++|||.||..|+..++...- + ..+.||.
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~--~--~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPS--G--SGFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSS--S--ST---SS
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccC--C--cCCCCcC
Confidence 89999997 6899999999999999999987521 1 2378886
No 8
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.26 E-value=4.4e-07 Score=61.20 Aligned_cols=37 Identities=30% Similarity=0.872 Sum_probs=28.8
Q ss_pred ccccccccccCCc-eecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 119 CDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 119 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
|+||++.+. ++ +.++|||.||.+||.+|+... .+||.
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 899999863 45 678999999999999998751 57876
No 9
>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=98.25 E-value=4.9e-07 Score=62.71 Aligned_cols=40 Identities=38% Similarity=0.836 Sum_probs=32.8
Q ss_pred cccccccccc-cCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 118 MCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 118 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
+|+||++++. ...++.++|||.||.+|+..|+... .+||.
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 4567778999999999999999762 28887
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=98.25 E-value=8.2e-07 Score=60.54 Aligned_cols=39 Identities=31% Similarity=0.867 Sum_probs=31.9
Q ss_pred ccccccccccCCce-ecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 119 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 119 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
|+||++.+. .+. .++|||.||..||.+++.. . ..++||.
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 899999864 344 7899999999999999997 2 3478986
No 11
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.22 E-value=1.5e-06 Score=65.34 Aligned_cols=38 Identities=37% Similarity=0.872 Sum_probs=34.4
Q ss_pred CCcCCC--CCCCCccccC--CCCceEe-ccccceecccccccc
Q 011726 275 HTKPCP--KCHKPVEKNG--GCNLVSC-ICGQAFCWLCGGATG 312 (478)
Q Consensus 275 ~~k~CP--~C~~~IeK~~--GCnhm~C-~C~~~FCw~C~~~~~ 312 (478)
+.+.|| +|+..|+..+ |.++|+| .|++.|||.|+.+|+
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 9999999864 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=98.18 E-value=7.7e-07 Score=66.93 Aligned_cols=38 Identities=42% Similarity=1.069 Sum_probs=28.6
Q ss_pred CCcCCCC--CCCCccccCCCCc--eEec-cccceecccccccc
Q 011726 275 HTKPCPK--CHKPVEKNGGCNL--VSCI-CGQAFCWLCGGATG 312 (478)
Q Consensus 275 ~~k~CP~--C~~~IeK~~GCnh--m~C~-C~~~FCw~C~~~~~ 312 (478)
+.+.||+ |...|.+..|.++ |+|. |++.|||.|+++|+
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 4589988 9999999999999 9996 99999999999974
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=1.5e-06 Score=76.81 Aligned_cols=52 Identities=25% Similarity=0.685 Sum_probs=41.3
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
...+.||||++.+....+++..|||.||..|++.-+.. ..+||. |...++..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k 180 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHK 180 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchh
Confidence 45689999999998777788999999999999987764 258999 55455443
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.07 E-value=3.1e-06 Score=76.81 Aligned_cols=65 Identities=23% Similarity=0.532 Sum_probs=47.1
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhc--------CCcccccCCCcccCCccCHHHHHHHhc
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE--------GQSKRIRCMAHKCNAICDEAVVRNLVS 182 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~--------g~~~~i~CP~~~C~~~~~~~~i~~ll~ 182 (478)
.+.++|+||++.+ .+++.++|||.||..|+..|+...-.. ......+||. |...+....+..+..
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 567778999999999999998642110 0113579999 999887765544443
No 15
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.07 E-value=2.1e-06 Score=58.85 Aligned_cols=41 Identities=32% Similarity=0.783 Sum_probs=22.8
Q ss_pred cccccccccc--CCceecCCCCccchhhHHHHHHHHHhcCCcccccCC
Q 011726 119 CDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCM 164 (478)
Q Consensus 119 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP 164 (478)
|+||.+ +.. ..+..|+|||.||++|+.+.+.... ...++||
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 2367789999999999999988532 1358887
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.93 E-value=6.2e-06 Score=57.13 Aligned_cols=42 Identities=31% Similarity=0.895 Sum_probs=33.4
Q ss_pred ccccccccccc-CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccC
Q 011726 118 MCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (478)
Q Consensus 118 ~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~ 169 (478)
.|+||++.+.. ..+..++|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 49999999833 456667999999999999987 13589998 64
No 17
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.90 E-value=9.8e-06 Score=57.80 Aligned_cols=46 Identities=26% Similarity=0.745 Sum_probs=35.9
Q ss_pred cccccccccccccCCceecCCCCc-cchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
...|.||++.. ..++.++|||. ||..|+..++. ...+||. |...+.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 46899999984 46777899999 99999999988 2368998 877653
No 18
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.89 E-value=1.2e-05 Score=55.28 Aligned_cols=44 Identities=32% Similarity=0.851 Sum_probs=32.8
Q ss_pred cccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 118 MCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
+|+||++.+. ......+|||.||..|+..++.. + ..+||. |...
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 33334469999999999999875 2 367987 7653
No 19
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.65 E-value=4e-05 Score=50.70 Aligned_cols=38 Identities=34% Similarity=0.865 Sum_probs=30.4
Q ss_pred ccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
|+||++. ...+..++|||.||..|+..++. .+ ...||.
T Consensus 1 C~iC~~~--~~~~~~~~C~H~~c~~C~~~~~~----~~---~~~CP~ 38 (39)
T smart00184 1 CPICLEE--LKDPVVLPCGHTFCRSCIRKWLK----SG---NNTCPI 38 (39)
T ss_pred CCcCccC--CCCcEEecCCChHHHHHHHHHHH----hC---cCCCCC
Confidence 7899988 35677789999999999999987 12 357875
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.2e-05 Score=72.63 Aligned_cols=55 Identities=25% Similarity=0.567 Sum_probs=43.9
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i 177 (478)
...++|.||++.. .+++...|||.||-.|+-+|+..... .-.||. |+..++.+.+
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~-----~~~cPV--CK~~Vs~~~v 99 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPN-----SKECPV--CKAEVSIDTV 99 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCC-----CeeCCc--cccccccceE
Confidence 4679999999984 67888899999999999999987532 246888 8877766544
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=97.63 E-value=6.1e-05 Score=56.32 Aligned_cols=48 Identities=8% Similarity=0.134 Sum_probs=38.4
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHH
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~ 176 (478)
+.|+||.+.+ .+++.++|||.||+.|+..|+.. + ..||. |+..++.+.
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~----~----~~cP~--~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS----H----GTDPV--TGQPLTHED 49 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH----C----CCCCC--CcCCCChhh
Confidence 5799999986 56788899999999999999975 1 37988 666665443
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=97.59 E-value=4.1e-05 Score=70.32 Aligned_cols=55 Identities=27% Similarity=0.521 Sum_probs=38.7
Q ss_pred cccccccccccccc-----cCCc--eecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 114 SSTVMCDICMEEVA-----GDKA--TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 114 ~~~~~C~IC~e~~~-----~~~~--~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
+...+|+||++..- .... +..+|+|.||..|++.|-..+-..| ..-.||. |...+
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f 229 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRF 229 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Cccee
Confidence 45689999999852 1222 2339999999999999998653222 2457999 87654
No 23
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.57 E-value=3.2e-05 Score=79.08 Aligned_cols=59 Identities=20% Similarity=0.522 Sum_probs=44.9
Q ss_pred cccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHh
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLV 181 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll 181 (478)
...||||++..+ -+..+.|||.||-.|+-+||...... .+..||. |...+....+.-+.
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeee
Confidence 678999999843 34556799999999999999987322 3578999 98888775554443
No 24
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.49 E-value=7.5e-05 Score=70.76 Aligned_cols=48 Identities=27% Similarity=0.604 Sum_probs=35.9
Q ss_pred ccccccccccccccCC------ceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVAGDK------ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...+|+||++.+.... .+..+|+|.||..|+..|+.. ...||. |...+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~ 226 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPF 226 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEe
Confidence 4579999999864322 234589999999999998753 248999 87654
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=7e-05 Score=71.37 Aligned_cols=50 Identities=28% Similarity=0.652 Sum_probs=41.0
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~ 176 (478)
....|.+|++.. .++..++|||.||-+|+..|...+ -.||. |...+.+..
T Consensus 238 a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek--------~eCPl--CR~~~~psk 287 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEK--------AECPL--CREKFQPSK 287 (293)
T ss_pred CCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHccc--------cCCCc--ccccCCCcc
Confidence 457899999984 578888999999999999998763 24998 888776654
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.34 E-value=0.00015 Score=73.85 Aligned_cols=50 Identities=26% Similarity=0.616 Sum_probs=39.7
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
...+.|+||.+.+ ..++.++|||.||..|+..|+.. ...||. |...+...
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQES 73 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccc
Confidence 3568999999987 46677899999999999999864 137998 88766543
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=0.00012 Score=72.57 Aligned_cols=43 Identities=30% Similarity=0.845 Sum_probs=36.7
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccC
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~ 169 (478)
+...|+||++.+. .+..++|||.||..|+...+. ..+.||. |.
T Consensus 12 ~~~~C~iC~~~~~--~p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFR--EPVLLPCGHNFCRACLTRSWE--------GPLSCPV--CR 54 (386)
T ss_pred ccccChhhHHHhh--cCccccccchHhHHHHHHhcC--------CCcCCcc--cC
Confidence 5689999999984 447789999999999999998 2489998 77
No 28
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.19 E-value=0.0013 Score=65.73 Aligned_cols=34 Identities=18% Similarity=0.586 Sum_probs=28.7
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFI 150 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~ 150 (478)
+...|+||..-+ .+++.|+|+|..|+-|-+..+.
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhcc
Confidence 467899998876 5789999999999999886654
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.18 E-value=0.00027 Score=68.51 Aligned_cols=63 Identities=22% Similarity=0.595 Sum_probs=48.5
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHH--HhcCCCchHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRN--LVSKKHPNLAEKF 192 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~--ll~~~~~e~~~~y 192 (478)
...-|.||++-| .-+...+|+|.||.-|++.|+.. ...||. |...+....++. +| .++++-|
T Consensus 22 ~lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il----~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRIL----DEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHh--cCceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHH----HHHHHHH
Confidence 456799999987 34566789999999999999975 367998 998888877753 34 3666665
Q ss_pred H
Q 011726 193 E 193 (478)
Q Consensus 193 ~ 193 (478)
.
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=96.89 E-value=0.00061 Score=49.82 Aligned_cols=47 Identities=21% Similarity=0.522 Sum_probs=30.4
Q ss_pred ccccccccccccccCCce-ecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccC
Q 011726 115 STVMCDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~ 169 (478)
..+.|||....+ .+++ +..|||.|.++.+.+||. . ...++||..||.
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~----~--~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQ----R--NGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCT----T--TS-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHH----h--cCCCCCCCCCCC
Confidence 458899999886 4554 469999999999999992 1 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=96.87 E-value=0.00067 Score=66.31 Aligned_cols=53 Identities=23% Similarity=0.468 Sum_probs=36.8
Q ss_pred cccccccccccc-CCc--eecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHH
Q 011726 117 VMCDICMEEVAG-DKA--TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (478)
Q Consensus 117 ~~C~IC~e~~~~-~~~--~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (478)
..||+|..+... ..+ ...+|||.||.+|+...|.. | +..||. |...+....++
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 579999997322 222 11279999999999999742 3 358996 98877665443
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.81 E-value=0.00034 Score=75.16 Aligned_cols=55 Identities=25% Similarity=0.682 Sum_probs=44.7
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNL 180 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~l 180 (478)
....||+|.+- ..+.+...|||.||..|++..+.+. .=+||. |+..|+..+|..+
T Consensus 642 ~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETR-------QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHh-------cCCCCC--CCCCCCccccccc
Confidence 56899999944 3677888999999999999999873 248998 9998888776543
No 33
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.0011 Score=63.58 Aligned_cols=52 Identities=23% Similarity=0.536 Sum_probs=41.9
Q ss_pred ccccccccccccccc-CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCH
Q 011726 114 SSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~ 174 (478)
....+|.||++.+.. +....++|.|.|...|+.+|+.. ...+||. |...+++
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 456899999999754 45566799999999999999874 3468998 9887764
No 34
>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=96.49 E-value=0.0083 Score=41.16 Aligned_cols=39 Identities=23% Similarity=0.429 Sum_probs=33.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcC
Q 011726 53 EDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENG 91 (478)
Q Consensus 53 ~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~~~ 91 (478)
+.|...+++.|+++..|..+|...+||.+.-++.||+.+
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 568889999999999999999999999999999999743
No 35
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.46 E-value=0.00046 Score=50.88 Aligned_cols=46 Identities=22% Similarity=0.621 Sum_probs=22.5
Q ss_pred cccccccccccccCCceec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 116 TVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
..-|++|.+.+ ..++.+ .|.|.||..|++..+. ..||. |..+....
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~q 53 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQ 53 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-S-S
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC----------CCCCC--cCChHHHH
Confidence 45799999985 577776 9999999999966332 35998 87655333
No 36
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.39 E-value=0.0017 Score=66.45 Aligned_cols=55 Identities=20% Similarity=0.500 Sum_probs=43.6
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
.....|.+|-++- .+.+...|.|.||+-|++.|+.....+. .+.||. |...++.+
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 3568999998873 5677789999999999999998765433 389998 88766544
No 37
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.27 E-value=0.0025 Score=63.38 Aligned_cols=45 Identities=29% Similarity=0.649 Sum_probs=36.9
Q ss_pred cccccccccccc-CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
.+|.||+|+|.. +....|+|+|.|...|+..||... .-.||. |+.
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 699999999865 455668999999999999999863 236999 655
No 38
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.08 E-value=0.0032 Score=48.66 Aligned_cols=50 Identities=12% Similarity=0.109 Sum_probs=36.9
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
+.+.|+|+.+.+ .+++.+++||.|++.++..|+.. ....||. |+..+...
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 468999999985 68899999999999999999976 2357888 56666543
No 39
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0052 Score=58.16 Aligned_cols=53 Identities=30% Similarity=0.567 Sum_probs=40.0
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i 177 (478)
..+.|.||++.. ..+..++|||.||..|+-..+..+ ..-.||. |...+.+..|
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 467899999973 567788999999999999865432 2346998 8876665544
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=95.98 E-value=0.0034 Score=48.52 Aligned_cols=41 Identities=24% Similarity=0.486 Sum_probs=28.9
Q ss_pred cccccccccccc----------CCc-eecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 117 VMCDICMEEVAG----------DKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 117 ~~C~IC~e~~~~----------~~~-~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
..|.||++.+.. ..+ ....|||.|...|+.+++... -.||.
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 234899999999999999641 28887
No 41
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.76 E-value=0.3 Score=49.79 Aligned_cols=117 Identities=21% Similarity=0.401 Sum_probs=68.8
Q ss_pred eeCHHHHHHHHHHHHHHHHHHcCCCHH--HHHHHHHHcCCChHHHHHHHHh-cCch------hhhh-----hcCCCc--c
Q 011726 41 VITRESLLAAQKEDLRRVMELLSLREH--HARTLLIHYRWDVEKLLAVLVE-NGKE------SLFN-----EAGVTV--I 104 (478)
Q Consensus 41 vl~~~~i~~~~~~~i~~v~~~l~i~~~--~a~~lL~~~~W~~e~l~e~~~~-~~~~------~~~~-----~~gl~~--~ 104 (478)
.+|..+|+.-+...+..|+.|.-|..+ +-..+|+.|+=..+.. .-|.+ +|.. .+.. .+.+.- +
T Consensus 85 ~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~-~Fy~efNGk~Fn~le~e~Chll~V~~ve~~~s~d 163 (493)
T KOG0804|consen 85 YMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADAD-TFYEEFNGKQFNSLEPEVCHLLYVDRVEVTESED 163 (493)
T ss_pred cccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHH-HHHHHcCCCcCCCCCccceeEEEEEEEEEEeccc
Confidence 479999999988888888887766532 2355666776554431 22221 2211 0111 001110 0
Q ss_pred CCCCCCCCccccccccccccccccC--CceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 105 DDADPMLPLSSTVMCDICMEEVAGD--KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 105 ~~~~~~~~~~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..+.++....+..+||||++-...+ -+.+..|.|.|.-.|+..|+. ..||. |..
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 1111222334678999999987532 235569999999999988753 58988 654
No 42
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.35 E-value=0.0091 Score=45.70 Aligned_cols=57 Identities=25% Similarity=0.408 Sum_probs=26.4
Q ss_pred cccccccccccc-cCCc--ee---cCCCCccchhhHHHHHHHHHhcCCcc-cc--cCCCcccCCccCH
Q 011726 116 TVMCDICMEEVA-GDKA--TK---MDCGHCFCNDCWTEHFIVKINEGQSK-RI--RCMAHKCNAICDE 174 (478)
Q Consensus 116 ~~~C~IC~e~~~-~~~~--~~---l~CgH~fC~~C~~~yi~~~i~~g~~~-~i--~CP~~~C~~~~~~ 174 (478)
...|+||+.... .... .. ..|++.|...||.+|+...-.....+ ++ .||. |...+..
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 468999998753 2221 11 26899999999999998765543322 32 6998 8877643
No 43
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.95 E-value=0.024 Score=53.94 Aligned_cols=50 Identities=22% Similarity=0.541 Sum_probs=37.4
Q ss_pred cccccccccccccccCCcee-cCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 114 SSTVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
+...+|++|.+. +..|.. .+|||.||--|+..-.... ..+.||. |+..+.
T Consensus 237 t~~~~C~~Cg~~--PtiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEP--PTIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred cCCceeeccCCC--CCCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 356899999875 344444 4799999999999876642 3489998 887665
No 44
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.82 E-value=0.026 Score=57.96 Aligned_cols=41 Identities=32% Similarity=0.754 Sum_probs=33.3
Q ss_pred CCcccCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCC
Q 011726 205 KMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSP 249 (478)
Q Consensus 205 ~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~ 249 (478)
...+.|| .|+..|....+ -..++|.||+.||..|+.+|+..
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 4567898 79998876555 56689999999999999888654
No 45
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.79 E-value=0.14 Score=51.58 Aligned_cols=38 Identities=37% Similarity=0.797 Sum_probs=34.7
Q ss_pred hCCcCCCC--CCCCccccCCCCceEe-ccccceeccccccc
Q 011726 274 VHTKPCPK--CHKPVEKNGGCNLVSC-ICGQAFCWLCGGAT 311 (478)
Q Consensus 274 ~~~k~CP~--C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~ 311 (478)
.+.+-||+ |..|+-...|++-..| +|.+-||.+|...|
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 45689998 9999977999999999 79999999999986
No 46
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.79 E-value=0.013 Score=55.99 Aligned_cols=47 Identities=28% Similarity=0.594 Sum_probs=36.0
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
...-|-||-+-+ .-+...+|||.||.-|++.|+.. ...||. |.....
T Consensus 24 s~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPC 70 (391)
T ss_pred hHHHhhhhhhee--ecceecccccchhHHHHHHHhcC--------CCCCcc--ccccHH
Confidence 356799998876 34566799999999999999874 357887 765443
No 47
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.66 E-value=0.018 Score=55.48 Aligned_cols=54 Identities=20% Similarity=0.431 Sum_probs=41.2
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (478)
....+|+||+.+- ..++.|.|+|.||.-|++.-+.. +. ..|+. |...++...+.
T Consensus 5 ~~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 5 TKKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred ccCCcceeeeccC--CcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchhc
Confidence 3457899999883 56789999999999999876543 22 45988 98888766543
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.45 E-value=0.038 Score=55.40 Aligned_cols=54 Identities=26% Similarity=0.516 Sum_probs=37.1
Q ss_pred cccccccccccccccCC-----cee-cCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 114 SSTVMCDICMEEVAGDK-----ATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
+...+|+||++.+.... ... .+|.|.||..|++.|-...-. +....-.||. |..
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv 218 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRV 218 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccC
Confidence 56789999999864333 223 379999999999998643222 2223457998 765
No 49
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.16 E-value=0.038 Score=54.59 Aligned_cols=48 Identities=27% Similarity=0.630 Sum_probs=37.3
Q ss_pred ccccccccccc-cccC----------CceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEE-VAGD----------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~-~~~~----------~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
....|.||.++ +.+. .+..|+|||.+...|++.|++.+ -.||- |+.++
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ 344 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPV 344 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCcc
Confidence 45789999999 3322 24678999999999999999852 37998 77653
No 50
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.08 E-value=0.03 Score=39.13 Aligned_cols=44 Identities=25% Similarity=0.618 Sum_probs=21.0
Q ss_pred ccccccccccC--CceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 119 CDICMEEVAGD--KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 119 C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
|++|.+++... ++.-.+||+.+|+.||..-+.. + .=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~----~---~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN----E---GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS----S----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc----c---CCCCCC--CCCC
Confidence 78999887443 3344589999999999886552 1 237987 7654
No 51
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.04 E-value=0.028 Score=33.99 Aligned_cols=23 Identities=39% Similarity=0.953 Sum_probs=15.5
Q ss_pred cCCCCCCCCccccCCCCceEec-cccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~-C~~~F 303 (478)
|.||.|+..|.... ..|. |||.|
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 57888888885322 5663 77776
No 52
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=93.42 E-value=0.4 Score=47.01 Aligned_cols=80 Identities=16% Similarity=0.312 Sum_probs=48.1
Q ss_pred HHHHHHHhcCchhhhhhcCCCccCCCCC--------CCCccccccccccccccccCCceec-CCCCccchhhHHHHHHHH
Q 011726 82 KLLAVLVENGKESLFNEAGVTVIDDADP--------MLPLSSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVK 152 (478)
Q Consensus 82 ~l~e~~~~~~~~~~~~~~gl~~~~~~~~--------~~~~~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~ 152 (478)
++++-|+.++.++.. +.++.++.++++ .........|+||.... .++..+ --|=+||-.|+-+|+..
T Consensus 259 qfldWWyssd~~~~~-k~~l~~p~PpPPh~~~~se~e~l~~~~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~- 334 (357)
T KOG0826|consen 259 QFLDWWYSSDNQRKI-KSTLDPPIPPPPHKQYNSESELLPPDREVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVN- 334 (357)
T ss_pred HHHHHHhcchHHHhh-ccCCCCCCCcCChhhcccccccCCCccccChhHHhcc--CCCceEEecceEEeHHHHHHHHHh-
Confidence 345667754433333 335544433322 11123457899999875 233333 56999999999999983
Q ss_pred HhcCCcccccCCCcccCCcc
Q 011726 153 INEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 153 i~~g~~~~i~CP~~~C~~~~ 172 (478)
.| +||..+|+..+
T Consensus 335 --~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 335 --YG-----HCPVTGYPASV 347 (357)
T ss_pred --cC-----CCCccCCcchH
Confidence 33 68888776543
No 53
>PRK00420 hypothetical protein; Validated
Probab=93.40 E-value=0.63 Score=38.89 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=20.7
Q ss_pred CcCCCCCCCCccccCCCCceEeccccceecccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 310 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~ 310 (478)
...||.|+.|+.+. +=|..||..|+..
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 48999999997651 3357888899876
No 54
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.19 E-value=0.14 Score=58.70 Aligned_cols=75 Identities=24% Similarity=0.497 Sum_probs=57.2
Q ss_pred ccccccccccc-cccCCceecCCCCccchhhHHHHHHHHHhcCC--cccccCCCcccCCccCHHHHHHHhcCCCchHHHH
Q 011726 115 STVMCDICMEE-VAGDKATKMDCGHCFCNDCWTEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEK 191 (478)
Q Consensus 115 ~~~~C~IC~e~-~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~ 191 (478)
..-.|.|||.+ +.....+.|.|+|.|...|.+.-++..-.... +..|.||. |...+....++.++. .+.+.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLld----PiKel 3558 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLD----PIKEL 3558 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHH----HHHHH
Confidence 45689999988 44456678999999999999999887654433 23578999 999998888888886 34555
Q ss_pred HHHH
Q 011726 192 FERF 195 (478)
Q Consensus 192 y~~~ 195 (478)
|+..
T Consensus 3559 ~edV 3562 (3738)
T KOG1428|consen 3559 YEDV 3562 (3738)
T ss_pred HHHH
Confidence 5543
No 55
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.12 E-value=0.13 Score=52.72 Aligned_cols=49 Identities=24% Similarity=0.591 Sum_probs=36.6
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~ 174 (478)
...+.|.||+..+ -.++.++|||.||..|+.+-+. ....||. |...+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 3579999999886 4677889999999999766222 2357887 8876653
No 56
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.07 E-value=0.032 Score=50.36 Aligned_cols=33 Identities=27% Similarity=0.870 Sum_probs=27.1
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHF 149 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi 149 (478)
-+|.|.||-.++ ..++...|||.||..|...-+
T Consensus 195 IPF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 195 IPFLCGICKKDY--ESPVVTECGHSFCSLCAIRKY 227 (259)
T ss_pred Cceeehhchhhc--cchhhhhcchhHHHHHHHHHh
Confidence 358999999997 467888999999999975543
No 57
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.74 E-value=0.13 Score=50.92 Aligned_cols=55 Identities=27% Similarity=0.666 Sum_probs=40.6
Q ss_pred ccccccccccccC----CceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc--cCHHHHHHH
Q 011726 117 VMCDICMEEVAGD----KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI--CDEAVVRNL 180 (478)
Q Consensus 117 ~~C~IC~e~~~~~----~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~--~~~~~i~~l 180 (478)
..|.||-++++.. -+..|.|||.+|..|....+.. ..+.||. |... ++...++.+
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 2456789999999999988764 3477877 8776 555555443
No 58
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.46 E-value=0.089 Score=52.84 Aligned_cols=49 Identities=22% Similarity=0.672 Sum_probs=38.0
Q ss_pred ccccccccccccc---CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 116 TVMCDICMEEVAG---DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 116 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
..+||||++.+.. ..++++.|||.|=.+|++.|+. ++ ...+||. |...-
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 4689999998642 3567889999999999999993 22 4578998 77543
No 59
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.00 E-value=0.028 Score=55.35 Aligned_cols=47 Identities=30% Similarity=0.680 Sum_probs=34.6
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
..+.|+||++-+. .-+....|+|+||.+|+..-+.. |. -.||. |...
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 5689999999874 34455699999999998776543 32 37887 6653
No 60
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.95 E-value=0.73 Score=46.47 Aligned_cols=126 Identities=15% Similarity=0.204 Sum_probs=68.6
Q ss_pred eeeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhh-cCCC-------ccCCCCCCC
Q 011726 40 KVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNE-AGVT-------VIDDADPML 111 (478)
Q Consensus 40 ~vl~~~~i~~~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~~~~~~~~~~-~gl~-------~~~~~~~~~ 111 (478)
..|++......-..-+.+-..+||++.+..+-++...+-..=..+-.|. .++.. .|.- ++-.-....
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 3455555555566666777788888775555444433333222222222 11111 1110 000000000
Q ss_pred Ccccccccccccccccc-CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHH
Q 011726 112 PLSSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (478)
Q Consensus 112 ~~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i 177 (478)
..-..|.|||=-+..+. +.|..|.|||.+|++=+..... +|. ..++||- |+.....+..
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 11246899997666443 4567889999999998776543 344 4789998 8876555443
No 61
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.58 E-value=0.38 Score=46.77 Aligned_cols=94 Identities=23% Similarity=0.512 Sum_probs=55.4
Q ss_pred CCCCccchhhHHHHHHHHHhcCC--cccccCCCcccCCccCHHHHHHHhcCCCchHHHHHHHHHHHHHHhhCCCcccCCC
Q 011726 135 DCGHCFCNDCWTEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPS 212 (478)
Q Consensus 135 ~CgH~fC~~C~~~yi~~~i~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~ 212 (478)
.||-.||+.|+..|-...-..+. +.. ..|...+++... ...+|...... ......+.||
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t-----~tc~y~vde~~a----------~~arwd~as~~---TIk~tTkpCP- 401 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGT-----TTCAYRVDERAA----------EQARWDAASKE---TIKKTTKPCP- 401 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccc-----cceeeecChhhh----------hhhhhhhhhhh---hhhhccCCCC-
Confidence 49999999999999653322211 011 124444443221 12344433221 1223457888
Q ss_pred CCCCCceEEeccccceeeEe--c-CCccccccccCCCCCCC
Q 011726 213 TPHCGNAIRVEEVEVCEVEC--A-CGAQFCFSCLSEAHSPC 250 (478)
Q Consensus 213 ~p~C~~~i~~~~~~~~~v~C--~-C~~~fC~~C~~~~H~~~ 250 (478)
.|..+...++. ...+.| + ||..+||.|+.+|...+
T Consensus 402 --kChvptErnGG-CmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 402 --KCHVPTERNGG-CMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred --CccCccccCCc-eEEeecCCCCCCceeEeccCChhhhhh
Confidence 79877665543 345789 3 99999999999987643
No 62
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.18 E-value=0.15 Score=50.05 Aligned_cols=47 Identities=23% Similarity=0.628 Sum_probs=35.3
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...+|.+|-.-+- +......|-|.||++||-.|+.. ...||. |...+
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 4588999977652 33344589999999999999987 247998 66544
No 63
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=90.96 E-value=0.18 Score=39.79 Aligned_cols=31 Identities=19% Similarity=0.492 Sum_probs=24.5
Q ss_pred CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 135 DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 135 ~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
.|+|.|...|+.+++.++- + .-.||. |...+
T Consensus 51 ~C~H~FH~hCI~kWl~~~~--~---~~~CPm--CR~~w 81 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQS--S---KGQCPM--CRQPW 81 (85)
T ss_pred cCccHHHHHHHHHHHcccc--C---CCCCCC--cCCee
Confidence 7999999999999999751 1 247998 77654
No 64
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.23 E-value=0.16 Score=54.86 Aligned_cols=44 Identities=27% Similarity=0.728 Sum_probs=34.9
Q ss_pred ccccccccccccc-CC--ceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcc
Q 011726 116 TVMCDICMEEVAG-DK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHK 167 (478)
Q Consensus 116 ~~~C~IC~e~~~~-~~--~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~ 167 (478)
...|.||.+.... .+ +..++|+|.||..|++.|++. .-.||.+.
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~CR 337 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPTCR 337 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCcch
Confidence 5789999999642 11 567899999999999999987 14799833
No 65
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=89.92 E-value=0.07 Score=49.66 Aligned_cols=50 Identities=20% Similarity=0.483 Sum_probs=36.3
Q ss_pred ccccccccccccc-CCceec---CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 116 TVMCDICMEEVAG-DKATKM---DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 116 ~~~C~IC~e~~~~-~~~~~l---~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...||||-.+.-. -++..+ .|-|..|-+|.-.-++. .|..||-++|+.++
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence 3479999887321 233332 49999999999888764 35799999998754
No 66
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=89.57 E-value=0.37 Score=34.01 Aligned_cols=42 Identities=17% Similarity=0.377 Sum_probs=30.8
Q ss_pred cccccccccccCCceecCCC-----CccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 118 MCDICMEEVAGDKATKMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
.|-||++.....++...||. |.+...|+..|+..+- ..+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG------NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence 48899984334556666875 8899999999998642 247876
No 67
>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=89.48 E-value=0.14 Score=43.87 Aligned_cols=34 Identities=32% Similarity=0.703 Sum_probs=27.8
Q ss_pred ccccccccccccc-CCceecCCC------CccchhhHHHHH
Q 011726 116 TVMCDICMEEVAG-DKATKMDCG------HCFCNDCWTEHF 149 (478)
Q Consensus 116 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~yi 149 (478)
..+|.||++.+.. +-++.++|| |.||.+|++.|-
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 5789999999865 345666777 789999999994
No 68
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.46 E-value=0.16 Score=48.31 Aligned_cols=53 Identities=26% Similarity=0.606 Sum_probs=40.1
Q ss_pred ccccccccccccccC--------CceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHH
Q 011726 115 STVMCDICMEEVAGD--------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~ 175 (478)
+...|.||...+..+ +...|+|+|.|...|++.+... |+ .-.||- |+..++..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK--kqtCPY--CKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK--KQTCPY--CKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC--CCCCch--HHHHhhHh
Confidence 356799998875432 4678999999999999999764 22 358998 88877543
No 69
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.20 E-value=0.31 Score=34.60 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=19.8
Q ss_pred cCCCCCCCCccccC--CCCceEe-ccccce
Q 011726 277 KPCPKCHKPVEKNG--GCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~--GCnhm~C-~C~~~F 303 (478)
+.||.|+.++.... +-+++.| .||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46999999887543 3568999 499763
No 70
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.16 E-value=0.24 Score=48.76 Aligned_cols=51 Identities=29% Similarity=0.606 Sum_probs=37.5
Q ss_pred CccccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCH
Q 011726 112 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (478)
Q Consensus 112 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~ 174 (478)
|.++...|+||+-. +...+..+|+|.-|.+|+.+++.. .-+|.. |+..+..
T Consensus 418 p~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVID 468 (489)
T ss_pred CCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhc--------CCeeeE--ecceeee
Confidence 44577899999865 234455699999999999999864 236766 8876644
No 71
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=89.04 E-value=0.16 Score=50.82 Aligned_cols=46 Identities=30% Similarity=0.730 Sum_probs=33.8
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
.-|.||-+.- .++..-+|||..|..|+..|=.. .+|+ .||.++|..
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcEI 415 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCEI 415 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhccc--CCCC----CCCceeeEe
Confidence 4599998862 45555699999999999998543 2354 899966653
No 72
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.65 E-value=0.23 Score=51.11 Aligned_cols=51 Identities=22% Similarity=0.414 Sum_probs=36.3
Q ss_pred cccccccccccccccC-----Cc----------eecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 114 SSTVMCDICMEEVAGD-----KA----------TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~-----~~----------~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
..+..|+||+.+++.- .+ ...+|.|.|.+.|+.+++.. ..+.||. |..+++
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 4567899999986521 11 12399999999999999874 2468998 544443
No 73
>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=88.53 E-value=0.21 Score=49.10 Aligned_cols=53 Identities=28% Similarity=0.670 Sum_probs=34.9
Q ss_pred cCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEK 288 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 288 (478)
-|| .|..-....+.....+. +|||.||..|.... | ..+..+||.|+.++-+
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 588 68775555444333455 79999999997531 1 1123589999998886
Q ss_pred cC
Q 011726 289 NG 290 (478)
Q Consensus 289 ~~ 290 (478)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 53
No 74
>PHA00626 hypothetical protein
Probab=88.49 E-value=0.29 Score=34.99 Aligned_cols=30 Identities=27% Similarity=0.471 Sum_probs=22.0
Q ss_pred CCCCCCC-CccccCCCCc----eEe-ccccceeccc
Q 011726 278 PCPKCHK-PVEKNGGCNL----VSC-ICGQAFCWLC 307 (478)
Q Consensus 278 ~CP~C~~-~IeK~~GCnh----m~C-~C~~~FCw~C 307 (478)
.||+|+. -|-|++-|+. ..| .||+.|=-.=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 6999998 4888777654 778 4888875443
No 75
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.75 E-value=0.3 Score=28.59 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=7.9
Q ss_pred CCCCCCCCccc
Q 011726 278 PCPKCHKPVEK 288 (478)
Q Consensus 278 ~CP~C~~~IeK 288 (478)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 37888887764
No 76
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.53 E-value=0.59 Score=46.49 Aligned_cols=48 Identities=23% Similarity=0.538 Sum_probs=36.3
Q ss_pred cccccccccccccccCCceecCCCCc-cchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
+...+|.||+.+. .+.+.|+|.|. .|.+|-+..- ... =.||. |...+.
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 4467899999984 57788999997 8999987764 222 26998 887653
No 77
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=86.75 E-value=0.14 Score=48.13 Aligned_cols=45 Identities=24% Similarity=0.549 Sum_probs=32.5
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
+.|..|+---+...++.+.|+|+||..|.+.- .+-.||. |+..+.
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir 48 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSIR 48 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccC----------Ccccccc--ccceee
Confidence 56998887655455566699999999997542 2238988 887653
No 78
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.31 E-value=0.39 Score=50.54 Aligned_cols=38 Identities=34% Similarity=0.733 Sum_probs=32.4
Q ss_pred CcCCC--CCCCCccc-cCCCCceEeccccceeccccccccC
Q 011726 276 TKPCP--KCHKPVEK-NGGCNLVSCICGQAFCWLCGGATGR 313 (478)
Q Consensus 276 ~k~CP--~C~~~IeK-~~GCnhm~C~C~~~FCw~C~~~~~~ 313 (478)
.|-|| .|+..+.- .+.+.-+.|.||+.|||.|+.+|+.
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~ 198 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHS 198 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccC
Confidence 56676 59988887 8889999999999999999998754
No 79
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=86.06 E-value=0.5 Score=32.01 Aligned_cols=30 Identities=33% Similarity=0.604 Sum_probs=22.7
Q ss_pred HHHHhCCcCCCCCCCCccccCCCCceEec---cccce
Q 011726 270 NWITVHTKPCPKCHKPVEKNGGCNLVSCI---CGQAF 303 (478)
Q Consensus 270 ~~i~~~~k~CP~C~~~IeK~~GCnhm~C~---C~~~F 303 (478)
.|.....+.||+|++.- |+--+.|+ |++.|
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 35666789999999875 77778883 77665
No 80
>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=85.91 E-value=2.9 Score=27.34 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=27.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHH
Q 011726 53 EDLRRVMELLSLREHHARTLLIHYRWDVEKLLAV 86 (478)
Q Consensus 53 ~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~ 86 (478)
+.|..+.+. |.+...++..|+..+||++..++.
T Consensus 4 ~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 4 EKVQQLMEM-GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 567888888 999999999999999999987653
No 81
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.62 E-value=0.4 Score=33.96 Aligned_cols=27 Identities=26% Similarity=0.593 Sum_probs=19.6
Q ss_pred CCcCCCCCCC-CccccCCCCceEe-ccccce
Q 011726 275 HTKPCPKCHK-PVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 275 ~~k~CP~C~~-~IeK~~GCnhm~C-~C~~~F 303 (478)
..+.||+|+. .+.... +.++| +||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 4479999998 443333 68999 699875
No 82
>PLN03086 PRLI-interacting factor K; Provisional
Probab=85.54 E-value=1.9 Score=46.28 Aligned_cols=57 Identities=26% Similarity=0.570 Sum_probs=35.0
Q ss_pred ccccCCCcccCCccCHHHHHHHhcCCCchHHHHHHHHHHHHHHhhCCCcccCCCCCCCCceEEeccccceeeEec-CCcc
Q 011726 159 KRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (478)
Q Consensus 159 ~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 237 (478)
..+.||. |...++...+...+. .-.....-|| ..+|+..+....... ...|+ |+..
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 3568998 988877665543332 1223455799 457999887555322 24676 7665
Q ss_pred c
Q 011726 238 F 238 (478)
Q Consensus 238 f 238 (478)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 5
No 83
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.46 E-value=0.55 Score=51.42 Aligned_cols=24 Identities=46% Similarity=0.985 Sum_probs=16.1
Q ss_pred cCCCCCCCCccccCCCCceEeccccceeccccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~ 311 (478)
+.||+|+..+.. +..||..||.+.
T Consensus 28 ~~Cp~CG~~~~~-----------~~~fC~~CG~~~ 51 (645)
T PRK14559 28 KPCPQCGTEVPV-----------DEAHCPNCGAET 51 (645)
T ss_pred CcCCCCCCCCCc-----------ccccccccCCcc
Confidence 567777777653 345888887663
No 84
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=84.56 E-value=2.7 Score=35.48 Aligned_cols=110 Identities=15% Similarity=0.221 Sum_probs=51.0
Q ss_pred cCHHHHHHHhcC-CCchHHHHHHHHHHHHHHhhCCCcccCCCCCCCCceEEeccccceeeEecCCccccccccCCC--CC
Q 011726 172 CDEAVVRNLVSK-KHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEA--HS 248 (478)
Q Consensus 172 ~~~~~i~~ll~~-~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~--H~ 248 (478)
++....+++++. +|.+.+.+|...+..+ |.-...+. =| -=...+...+.....+.|.||++||-. ...| |.
T Consensus 17 l~w~qt~r~msa~kdhdrf~kylavlqdr-v~~~dpil-lp---vg~hlfi~qs~~~rv~rcecghsf~d~-r~nwkl~a 90 (165)
T COG4647 17 LPWPQTRRMMSAYKDHDRFFKYLAVLQDR-VDWDDPIL-LP---VGDHLFICQSAQKRVIRCECGHSFGDY-RENWKLHA 90 (165)
T ss_pred CCcHHHHHHHhccccHHHHHHHHHHHHhh-cccCCCee-ee---cCCcEEEEecccccEEEEeccccccCh-hhCceeee
Confidence 444556666662 3344445554443332 22111111 13 122333333333345799999999976 3444 33
Q ss_pred CCCcchhHH-HHHH-hhhhHHHHHHHHhCCcCCCCCCCCcc
Q 011726 249 PCSCSMWDL-WAKK-CRDESETVNWITVHTKPCPKCHKPVE 287 (478)
Q Consensus 249 ~~~C~~~~~-~~~~-~~~~~~~~~~i~~~~k~CP~C~~~Ie 287 (478)
...-..-.. .... -..+...-+|+...--.||.|+++.+
T Consensus 91 ~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 91 NIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred EEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 221111100 0000 01122234676666668999998877
No 85
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.11 E-value=0.62 Score=28.08 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=9.0
Q ss_pred cCCCCCCCCccc
Q 011726 277 KPCPKCHKPVEK 288 (478)
Q Consensus 277 k~CP~C~~~IeK 288 (478)
+.||+|+..|..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 678888887653
No 86
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.51 E-value=0.48 Score=45.86 Aligned_cols=44 Identities=27% Similarity=0.706 Sum_probs=33.8
Q ss_pred cccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
++-|.||-..+ ..++...|+|+||..|....+.. | -+|+. |...
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk----~----~~c~v--C~~~ 284 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK----G----EKCYV--CSQQ 284 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc----C----Cccee--cccc
Confidence 46799999987 57788899999999997766542 2 46776 7653
No 87
>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=81.84 E-value=1.4 Score=27.93 Aligned_cols=28 Identities=25% Similarity=0.655 Sum_probs=15.9
Q ss_pred CCcCCCCCCCCccccCCCCceEe-ccccc
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C-~C~~~ 302 (478)
+.+-||+|+.+.....|=--|.| .|++.
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 34778888888887777566888 47764
No 88
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=81.33 E-value=3.8 Score=39.81 Aligned_cols=38 Identities=21% Similarity=0.379 Sum_probs=31.1
Q ss_pred cccccccccccccCC-ceecCCCCccchhhHHHHHHHHH
Q 011726 116 TVMCDICMEEVAGDK-ATKMDCGHCFCNDCWTEHFIVKI 153 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yi~~~i 153 (478)
...|.||+--|...+ +...+|.|+|..-|+..||....
T Consensus 115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 467999988876665 55569999999999999998765
No 89
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=81.19 E-value=0.48 Score=52.18 Aligned_cols=46 Identities=26% Similarity=0.623 Sum_probs=35.3
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
..|.||.+ .+.++...|||.||.+||..+|...- ...||. |...+.
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLK 500 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc------CCCCcH--HHHHHH
Confidence 79999999 36778889999999999999987521 126666 765443
No 90
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=80.89 E-value=2 Score=41.58 Aligned_cols=48 Identities=25% Similarity=0.654 Sum_probs=32.9
Q ss_pred ccccccccc-ccCCceec--CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCH
Q 011726 118 MCDICMEEV-AGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (478)
Q Consensus 118 ~C~IC~e~~-~~~~~~~l--~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~ 174 (478)
.||+|-.+. -...++.+ +|+|..|.+|+-.-+.. .+-.|| +|..++.-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cp--eC~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCP--ECMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCC--cccchhhh
Confidence 589997763 22233332 99999999999887764 246798 49876543
No 91
>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=80.82 E-value=6.5 Score=26.48 Aligned_cols=37 Identities=24% Similarity=0.343 Sum_probs=32.3
Q ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 53 EDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 53 ~~i~~v~~~l-~i~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
+.|..+++++ +++++.....|..+++|++..++.+.+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 5688999999 799999999999999999999988774
No 92
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.73 E-value=1.5 Score=28.92 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=21.1
Q ss_pred ccCCCCCCCCceEEeccc----cceeeEec-CCccc
Q 011726 208 KWCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 238 (478)
..|| +|+..+.++++ ....|.|+ |++.|
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 79999987662 34568997 98876
No 93
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.60 E-value=0.56 Score=33.38 Aligned_cols=45 Identities=27% Similarity=0.478 Sum_probs=31.4
Q ss_pred ccccccccccccCCceecCCCCc-cchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 117 VMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
-+|.||++. +.+.+.-.|||. .|.+|-...+.. . .-.||. |..++
T Consensus 8 dECTICye~--pvdsVlYtCGHMCmCy~Cg~rl~~~--~-----~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEH--PVDSVLYTCGHMCMCYACGLRLKKA--L-----HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccC--cchHHHHHcchHHhHHHHHHHHHHc--c-----CCcCcc--hhhHH
Confidence 579999986 233444589997 899998887764 1 236887 76543
No 94
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=80.57 E-value=1.1 Score=46.24 Aligned_cols=43 Identities=30% Similarity=0.801 Sum_probs=33.4
Q ss_pred ccccccccccccccccCCcee-cCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 113 LSSTVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
..+...|++|...+. +++. ..|||.||..|+..+... ...||.
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~--------~~~cp~ 61 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN--------HQKCPV 61 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc--------CcCCcc
Confidence 346689999998863 4454 699999999999998775 246776
No 95
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=80.45 E-value=0.26 Score=47.50 Aligned_cols=35 Identities=31% Similarity=0.623 Sum_probs=26.1
Q ss_pred HHhCCcCCCCCCCCccccCCCCceEe-ccccceecccccccc
Q 011726 272 ITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATG 312 (478)
Q Consensus 272 i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~ 312 (478)
+..++.+|--|-...+ |-+| .|||-|||-|...|-
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 3445677777766654 4678 599999999999874
No 96
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=80.42 E-value=1.6 Score=28.64 Aligned_cols=28 Identities=29% Similarity=0.797 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEEecc----ccceeeEec-CCccc
Q 011726 208 KWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQF 238 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-C~~~f 238 (478)
..|| +|+..+.+++ .....+.|+ |++.|
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 3688 7999988765 344568997 98875
No 97
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.87 E-value=1.1 Score=42.23 Aligned_cols=53 Identities=8% Similarity=0.221 Sum_probs=38.3
Q ss_pred ccccccccccccccC-Cceec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHH
Q 011726 115 STVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i 177 (478)
..+.|+||-+.++.. ....| +|||++|.+|...+|.. ...||. |...+.+..|
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 568899999997543 23344 99999999999998863 245776 6666655443
No 98
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.74 E-value=1.3 Score=30.66 Aligned_cols=29 Identities=28% Similarity=0.614 Sum_probs=19.3
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccceec
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAFCW 305 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw 305 (478)
-.||+|+..++-..+=..++| .||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 478999888865444336788 48776543
No 99
>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=79.58 E-value=0.68 Score=38.15 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=26.0
Q ss_pred ccccccccccccccCCceecCCCCccchhhHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWT 146 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 146 (478)
+...|++|...+....+...||||.|+..|.+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 34569999999876666667999999999975
No 100
>PF04641 Rtf2: Rtf2 RING-finger
Probab=79.22 E-value=1.6 Score=42.48 Aligned_cols=58 Identities=21% Similarity=0.434 Sum_probs=42.5
Q ss_pred ccccccccccccccc-CCceec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhc
Q 011726 114 SSTVMCDICMEEVAG-DKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 182 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~-~~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 182 (478)
...+.|||...++.. ..++.+ +|||+|+..+++.. ..+ -.||. |+..+...+|-.|-+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-----k~~----~~Cp~--c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-----KKS----KKCPV--CGKPFTEEDIIPLNP 170 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-----ccc----ccccc--cCCccccCCEEEecC
Confidence 467899999999854 345555 99999999999987 111 25998 998887665544444
No 101
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=79.20 E-value=1.4 Score=28.67 Aligned_cols=27 Identities=37% Similarity=0.943 Sum_probs=17.5
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCcc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 237 (478)
++|| .|++.+.+..+....+.|. |++.
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 5898 7999998766443333675 7765
No 102
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=78.12 E-value=1.3 Score=32.95 Aligned_cols=34 Identities=26% Similarity=0.715 Sum_probs=13.4
Q ss_pred cCCCCCCCCccc---cCCCCceEec-cccc----eecccccc
Q 011726 277 KPCPKCHKPVEK---NGGCNLVSCI-CGQA----FCWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK---~~GCnhm~C~-C~~~----FCw~C~~~ 310 (478)
-+|++|...... .+||-|++|. |=.. -|.+|-.|
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 3778777762 4322 25555544
No 103
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.93 E-value=1.6 Score=36.45 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=25.6
Q ss_pred ccCCCCCCCCceEEecc-------ccceeeEec-CCccccccccCCCCC
Q 011726 208 KWCPSTPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~-------~~~~~v~C~-C~~~fC~~C~~~~H~ 248 (478)
..|- +|+..+.... .......|+ |+..||..|..-+|.
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 6877654321 112246797 999999999887775
No 104
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=77.81 E-value=1.1 Score=45.68 Aligned_cols=25 Identities=24% Similarity=0.699 Sum_probs=13.7
Q ss_pred CcCCCCCCCCcc-c--cCCC----CceEec-cc
Q 011726 276 TKPCPKCHKPVE-K--NGGC----NLVSCI-CG 300 (478)
Q Consensus 276 ~k~CP~C~~~Ie-K--~~GC----nhm~C~-C~ 300 (478)
.-+|--|+..+- + ..|| ||+.|+ |+
T Consensus 427 CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch 459 (468)
T KOG1701|consen 427 CYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCH 459 (468)
T ss_pred ceehhhcCccccccCCCCcceeccCceeechhh
Confidence 346666776665 3 3445 556553 54
No 105
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=77.41 E-value=1.8 Score=30.23 Aligned_cols=25 Identities=28% Similarity=0.622 Sum_probs=15.0
Q ss_pred cCCCCCCCCccccCCCCceEe-cccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQ 301 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~ 301 (478)
+.||+|+.-+.-..-=+...| +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 789999954332222235677 6775
No 106
>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=77.33 E-value=1.6 Score=27.32 Aligned_cols=26 Identities=27% Similarity=0.722 Sum_probs=12.7
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
-+||.|+....-.+|.+ |.| .|+++|
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 107
>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=77.16 E-value=8.7 Score=24.97 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHH
Q 011726 54 DLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLV 88 (478)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~ 88 (478)
.|+.+.+ +|.+...++..|...+||.++.++.++
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 4455555 599999999999999999999887665
No 108
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=76.69 E-value=1.1 Score=30.47 Aligned_cols=29 Identities=34% Similarity=0.725 Sum_probs=19.6
Q ss_pred CCCCCCCccccCCCCceEeccccceecccccccc
Q 011726 279 CPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (478)
Q Consensus 279 CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~ 312 (478)
||-|...+. +-++=.|||.||..|+..+-
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERLW 29 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHHH
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHHH
Confidence 566666555 22555799999999998863
No 109
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=76.53 E-value=4.3 Score=40.20 Aligned_cols=86 Identities=20% Similarity=0.405 Sum_probs=52.2
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCchHHHHHH
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFE 193 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~ 193 (478)
..-++||||++.+. ...+..+=||..|.+|-.. ..-+||. |...++ .++.+.-
T Consensus 46 ~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g--~~R~~am----------- 98 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG--NIRCRAM----------- 98 (299)
T ss_pred hhhccCchhhccCc-ccceecCCCcEehhhhhhh-----------hcccCCc--cccccc--cHHHHHH-----------
Confidence 35689999999874 2344455589999999762 3468998 988777 3444332
Q ss_pred HHHHHHHHhhCCCcccCCC-CCCCCceEEeccccceeeEe
Q 011726 194 RFLLESFIEDNKMVKWCPS-TPHCGNAIRVEEVEVCEVEC 232 (478)
Q Consensus 194 ~~~~~~~v~~~~~~~~CP~-~p~C~~~i~~~~~~~~~v~C 232 (478)
+.++++ .+..||+ .-+|...+........+-.|
T Consensus 99 EkV~e~------~~vpC~~~~~GC~~~~~Y~~~~~HE~~C 132 (299)
T KOG3002|consen 99 EKVAEA------VLVPCKNAKLGCTKSFPYGEKSKHEKVC 132 (299)
T ss_pred HHHHHh------ceecccccccCCceeecccccccccccc
Confidence 222222 2346773 23677666654433333444
No 110
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=76.39 E-value=1.9 Score=47.48 Aligned_cols=50 Identities=26% Similarity=0.440 Sum_probs=38.9
Q ss_pred ccccccccccccccC-Cceec-CCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 115 STVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
..++|.||++.+... .+.+. .|-|+|...|++.|....-.+|. ...+||.
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 568999999997654 44555 78999999999999998555544 4568886
No 111
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=76.14 E-value=0.92 Score=44.46 Aligned_cols=84 Identities=25% Similarity=0.598 Sum_probs=45.9
Q ss_pred CccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCchHHHHHHHHH-HHHHHh----hCCCcccCCC
Q 011726 138 HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIE----DNKMVKWCPS 212 (478)
Q Consensus 138 H~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~~~~-~~~~v~----~~~~~~~CP~ 212 (478)
-+||..|-..+.. .|+.||. |...+- ++ +.+.+.|.-+. ++.|.+ ...+...|-
T Consensus 276 Gy~CP~CkakvCs--------LP~eCpi--C~ltLV-------ss---~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf- 334 (378)
T KOG2807|consen 276 GYFCPQCKAKVCS--------LPIECPI--CSLTLV-------SS---PHLARSYHHLFPLKPFVEIPETEYNGSRFCF- 334 (378)
T ss_pred ceeCCcccCeeec--------CCccCCc--cceeEe-------cc---hHHHHHHHhhcCCcchhhccccccCCCccee-
Confidence 4677777554432 6788888 776431 11 33333343322 222322 222444575
Q ss_pred CCCCCceEEeccccceeeEec-CCccccccccCCCCC
Q 011726 213 TPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHS 248 (478)
Q Consensus 213 ~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~ 248 (478)
.|+.- ......++|. |...||..|..-.|.
T Consensus 335 --~C~~~----~~~~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 335 --ACQGE----LLSSGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred --eeccc----cCCCCcEEchhccceeeccchHHHHh
Confidence 57221 1233458996 999999999876554
No 112
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=75.45 E-value=1.3 Score=43.64 Aligned_cols=50 Identities=24% Similarity=0.513 Sum_probs=35.3
Q ss_pred cccccccccccccc--CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 115 STVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
+.-.|+.|.++... .+++..+||-..|+-||...-.. + .=+||. |....+
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~-l------ngrcpa--crr~y~ 64 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN-L------NGRCPA--CRRKYD 64 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhh-c------cCCChH--hhhhcc
Confidence 34459999998643 56777899999999999764322 2 347998 775443
No 113
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=75.38 E-value=1.5 Score=35.17 Aligned_cols=29 Identities=34% Similarity=0.715 Sum_probs=21.4
Q ss_pred CCCCCCCCc--cccCCCCceEec-cccceecc
Q 011726 278 PCPKCHKPV--EKNGGCNLVSCI-CGQAFCWL 306 (478)
Q Consensus 278 ~CP~C~~~I--eK~~GCnhm~C~-C~~~FCw~ 306 (478)
-||.|+.++ ++.+-||...|+ |+|.|=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 699998754 445559999995 99877443
No 114
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.09 E-value=2.1 Score=47.06 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=8.6
Q ss_pred cCCCCCCCCccc
Q 011726 277 KPCPKCHKPVEK 288 (478)
Q Consensus 277 k~CP~C~~~IeK 288 (478)
+.||+|+....+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 788888876653
No 115
>PHA03096 p28-like protein; Provisional
Probab=74.66 E-value=1.7 Score=42.65 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=29.0
Q ss_pred cccccccccccc----CCcee-c-CCCCccchhhHHHHHHHHH
Q 011726 117 VMCDICMEEVAG----DKATK-M-DCGHCFCNDCWTEHFIVKI 153 (478)
Q Consensus 117 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~C~~~yi~~~i 153 (478)
..|+||++..-. +..+. | .|.|.||..|++.+..++.
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 22333 4 8999999999999998865
No 116
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=74.15 E-value=9.2 Score=24.72 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=25.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHH
Q 011726 55 LRRVMELLSLREHHARTLLIHYRWDVEKLLAVL 87 (478)
Q Consensus 55 i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~ 87 (478)
|+.+.++ |++...|+..|...+||.++.++.+
T Consensus 5 v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 5 IDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4444443 8999999999999999999877654
No 117
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.92 E-value=2.3 Score=48.08 Aligned_cols=34 Identities=29% Similarity=0.658 Sum_probs=23.3
Q ss_pred CCCcccCCCCCCCCceEEeccccceeeEec-CCc-----cccccccCCCC
Q 011726 204 NKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGA-----QFCFSCLSEAH 247 (478)
Q Consensus 204 ~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~-----~fC~~C~~~~H 247 (478)
....+.|| .|+... ....|+ ||. .||..|+....
T Consensus 623 EVg~RfCp---sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 623 EIGRRKCP---SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cccCccCC---CCCCcC-------CcccCCCCCCCCCcceeCccccCcCC
Confidence 34567898 698763 236887 985 48888876543
No 118
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.45 E-value=0.96 Score=40.60 Aligned_cols=29 Identities=38% Similarity=1.017 Sum_probs=21.6
Q ss_pred cCCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCcc
Q 011726 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (478)
Q Consensus 233 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 287 (478)
.||+.||..|.+.+ ..++..||-|+..|-
T Consensus 150 kCGHvFC~~Cik~a--------------------------lk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 150 KCGHVFCSQCIKDA--------------------------LKNTNKCPTCRKKIT 178 (187)
T ss_pred ccchhHHHHHHHHH--------------------------HHhCCCCCCcccccc
Confidence 49999999996521 234589999997664
No 119
>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=73.07 E-value=2.1 Score=35.68 Aligned_cols=26 Identities=27% Similarity=0.792 Sum_probs=17.7
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
+.||+|++..---.- +-++| +||..|
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 679999987763222 66788 577665
No 120
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.51 E-value=1.2 Score=44.72 Aligned_cols=47 Identities=28% Similarity=0.668 Sum_probs=33.0
Q ss_pred cccccccccccccC-Cceec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccC
Q 011726 116 TVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (478)
Q Consensus 116 ~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~ 169 (478)
...|.||-+-+|.. +...+ .|||.|...|+.+|+...-. .-.||. |.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps-----~R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS-----NRGCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCc-----cCCCCc--ee
Confidence 35799996655543 44455 49999999999999975322 136887 55
No 121
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=72.46 E-value=1.6 Score=31.34 Aligned_cols=45 Identities=27% Similarity=0.645 Sum_probs=30.6
Q ss_pred cccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCH
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~ 174 (478)
...|-.|... ......++|||..|..||-.- ..-.||. |...+..
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEF 51 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChh----------hccCCCC--CCCcccC
Confidence 3566666554 244567899999999998542 2246998 8876643
No 122
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=70.68 E-value=3.3 Score=31.16 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=19.4
Q ss_pred CCcCCCCCCCCccccCCCCceEec-cccc
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSCI-CGQA 302 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C~-C~~~ 302 (478)
.++.||.|+....+...=..++|. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 468999999999984443456663 6654
No 123
>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=70.60 E-value=3 Score=27.92 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=25.4
Q ss_pred cCCCCCCCC-ccccCCCCceEe-ccccceeccccccccCCC
Q 011726 277 KPCPKCHKP-VEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (478)
Q Consensus 277 k~CP~C~~~-IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H 315 (478)
..|+.|... +. ++| .|+..+|..|....+.+|
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 689999877 77 999 599999999988754444
No 124
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=70.49 E-value=2.7 Score=40.69 Aligned_cols=43 Identities=26% Similarity=0.765 Sum_probs=32.1
Q ss_pred ccccccccccccCCcee-cCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..|+.|-..+ .++.. -.|+|.||..|+..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 6799998765 24444 489999999999876654 3579998 764
No 125
>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=70.45 E-value=4.4 Score=26.57 Aligned_cols=27 Identities=33% Similarity=0.870 Sum_probs=18.9
Q ss_pred cCCCCCCCCceEEeccc----cceeeEec-CCccc
Q 011726 209 WCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 238 (478)
-|| .|+..+.+.+. ....+.|+ |++.|
T Consensus 4 ~CP---~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCP---NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECC---CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 587 79998887652 23358887 88764
No 126
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=69.62 E-value=2.8 Score=30.50 Aligned_cols=6 Identities=67% Similarity=2.084 Sum_probs=2.9
Q ss_pred CCCCCC
Q 011726 278 PCPKCH 283 (478)
Q Consensus 278 ~CP~C~ 283 (478)
+||+|+
T Consensus 29 ~CPnCG 34 (61)
T COG2888 29 PCPNCG 34 (61)
T ss_pred eCCCCC
Confidence 444444
No 127
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=69.33 E-value=1.3 Score=43.80 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=22.5
Q ss_pred CcCCCCCCCCccc-cCCCCceEe-ccccce
Q 011726 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (478)
Q Consensus 276 ~k~CP~C~~~IeK-~~GCnhm~C-~C~~~F 303 (478)
|.+||+|+..|-+ .-.=|.+.| +|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 5899999998864 455577899 599998
No 128
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=69.32 E-value=1.9 Score=47.21 Aligned_cols=47 Identities=28% Similarity=0.722 Sum_probs=29.4
Q ss_pred cccCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCc
Q 011726 207 VKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPV 286 (478)
Q Consensus 207 ~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~I 286 (478)
+..|| -|+ .++++. |.=.|||.||+.|-.. .+....+.||+|+.+.
T Consensus 643 ~LkCs---~Cn--~R~Kd~----vI~kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 643 LLKCS---VCN--TRWKDA----VITKCGHVFCEECVQT-------------------------RYETRQRKCPKCNAAF 688 (698)
T ss_pred ceeCC---Ccc--CchhhH----HHHhcchHHHHHHHHH-------------------------HHHHhcCCCCCCCCCC
Confidence 45788 586 222221 1113999999999753 0112348999999876
Q ss_pred c
Q 011726 287 E 287 (478)
Q Consensus 287 e 287 (478)
-
T Consensus 689 g 689 (698)
T KOG0978|consen 689 G 689 (698)
T ss_pred C
Confidence 5
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=68.28 E-value=4 Score=47.32 Aligned_cols=9 Identities=44% Similarity=1.427 Sum_probs=5.6
Q ss_pred ccCCCCCCCCce
Q 011726 208 KWCPSTPHCGNA 219 (478)
Q Consensus 208 ~~CP~~p~C~~~ 219 (478)
+.|| .|+..
T Consensus 668 rkCP---kCG~~ 676 (1337)
T PRK14714 668 RRCP---SCGTE 676 (1337)
T ss_pred EECC---CCCCc
Confidence 5676 57654
No 130
>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=66.71 E-value=22 Score=23.90 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=33.0
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 52 KEDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 52 ~~~i~~v~~~l-~i~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
.+.+..+++++ +++...++..|..++++++..++.+.+
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 45678888888 799999999999999999999988763
No 131
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=66.71 E-value=2.5 Score=42.45 Aligned_cols=47 Identities=23% Similarity=0.625 Sum_probs=36.8
Q ss_pred cccccccccccccc--CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccC
Q 011726 115 STVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (478)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~ 169 (478)
....|..|.+.+.. +....|+|.|.|...|+..|+.. ++ +-.||. |.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Cr 412 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CR 412 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HH
Confidence 45789999998653 45677899999999999999943 33 468988 76
No 132
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.60 E-value=4.1 Score=37.86 Aligned_cols=55 Identities=20% Similarity=0.409 Sum_probs=41.7
Q ss_pred cccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...|..|-.++...+.+.|.|-|.|.-.|+...-..--.+..-....||. |...+
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 35699999998888999999999999999998765432222223568998 88744
No 133
>PF14369 zf-RING_3: zinc-finger
Probab=66.19 E-value=4.8 Score=26.19 Aligned_cols=28 Identities=29% Similarity=0.883 Sum_probs=19.0
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCccc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQF 238 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~f 238 (478)
-||- .|...|.........+.|| |+..|
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 4997 7999998754333335687 77655
No 134
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=66.16 E-value=3.2 Score=46.60 Aligned_cols=26 Identities=38% Similarity=1.064 Sum_probs=22.4
Q ss_pred cCCCCCCCCccccCCCCceEec-ccccee
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAFC 304 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~-C~~~FC 304 (478)
..||.|+..+...+||. +|+ ||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999995 995 998766
No 135
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=66.06 E-value=2 Score=39.46 Aligned_cols=32 Identities=31% Similarity=0.739 Sum_probs=23.7
Q ss_pred CcCCCCCCCCccccCCCCceEeccccceecccccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~ 312 (478)
.-.||-|.-.+.. . +.=.|||.|||.|...|-
T Consensus 18 ~~~CpICld~~~d--P---VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRD--P---VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCC--c---EEcCCCchhHHHHHHHHH
Confidence 3589999887642 1 333699999999998873
No 136
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.26 E-value=7 Score=37.73 Aligned_cols=54 Identities=24% Similarity=0.516 Sum_probs=39.3
Q ss_pred cccccccccccccccCCceecC--CCCccchhhHHHHHHHHHhcCCcccccCCCc-ccCC
Q 011726 114 SSTVMCDICMEEVAGDKATKMD--CGHCFCNDCWTEHFIVKINEGQSKRIRCMAH-KCNA 170 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~-~C~~ 170 (478)
.....|.+|-+-+..+.++..+ =.|.||..|-++.|+.+-..| .+.||.. +|..
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 3568999999987544444432 269999999999999865555 4888863 5764
No 137
>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=64.90 E-value=4.2 Score=30.85 Aligned_cols=32 Identities=38% Similarity=0.942 Sum_probs=21.2
Q ss_pred CCCCCCCCccccCCCCceEe-ccccc-----eeccccccc
Q 011726 278 PCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGAT 311 (478)
Q Consensus 278 ~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~~ 311 (478)
.||.|+.+++..+ .+.+| .|+.. +|..|+.+.
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 68999 58854 699998774
No 138
>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=64.15 E-value=2.7 Score=29.85 Aligned_cols=35 Identities=20% Similarity=0.562 Sum_probs=17.3
Q ss_pred CCCceEEecc---ccceeeEec-CCccccccccCCCCCC
Q 011726 215 HCGNAIRVEE---VEVCEVECA-CGAQFCFSCLSEAHSP 249 (478)
Q Consensus 215 ~C~~~i~~~~---~~~~~v~C~-C~~~fC~~C~~~~H~~ 249 (478)
+|...+.... .......|+ |+..||..|-.=.|..
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 4655544322 113457998 9999999998777763
No 139
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=63.84 E-value=1.8 Score=42.65 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=17.5
Q ss_pred CcCCCCCCCCccc-cCCCCceEe-ccccce
Q 011726 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (478)
Q Consensus 276 ~k~CP~C~~~IeK-~~GCnhm~C-~C~~~F 303 (478)
|.+||+|+..|.+ .-.=|...| .|+|+|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3677777776653 344555677 477765
No 140
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.76 E-value=2 Score=40.34 Aligned_cols=17 Identities=35% Similarity=0.937 Sum_probs=14.2
Q ss_pred ccccceeccccccccCC
Q 011726 298 ICGQAFCWLCGGATGRD 314 (478)
Q Consensus 298 ~C~~~FCw~C~~~~~~~ 314 (478)
-|||.|||-|+-.|-..
T Consensus 64 lCGHLFCWpClyqWl~~ 80 (230)
T KOG0823|consen 64 LCGHLFCWPCLYQWLQT 80 (230)
T ss_pred ecccceehHHHHHHHhh
Confidence 39999999999998543
No 141
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.70 E-value=7.2 Score=26.86 Aligned_cols=28 Identities=32% Similarity=0.901 Sum_probs=20.5
Q ss_pred cCCCCCCCCceEEeccccceeeEec-CCccccc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCF 240 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~ 240 (478)
.|| +|+..+..+.... .+.|| ||..+=.
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 7999888776543 57898 8887644
No 142
>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=63.70 E-value=5.9 Score=28.28 Aligned_cols=11 Identities=45% Similarity=0.942 Sum_probs=8.7
Q ss_pred cCCCCCCCCcc
Q 011726 277 KPCPKCHKPVE 287 (478)
Q Consensus 277 k~CP~C~~~Ie 287 (478)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 89999986544
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=63.21 E-value=5.1 Score=27.09 Aligned_cols=22 Identities=36% Similarity=1.126 Sum_probs=16.3
Q ss_pred cCCCCCCCCccc-cCCCCceEe-ccc
Q 011726 277 KPCPKCHKPVEK-NGGCNLVSC-ICG 300 (478)
Q Consensus 277 k~CP~C~~~IeK-~~GCnhm~C-~C~ 300 (478)
..||.|+.|+-+ ..| .++| .|+
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 454 4667 363
No 144
>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=63.20 E-value=5.9 Score=25.80 Aligned_cols=31 Identities=19% Similarity=0.450 Sum_probs=24.1
Q ss_pred CCCCCCC-CccccCCCCceEe-ccccceeccccccccCCC
Q 011726 278 PCPKCHK-PVEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (478)
Q Consensus 278 ~CP~C~~-~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H 315 (478)
.||.|+. ++. ++| .|+...|..|....+.+|
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 5888877 888 999 599999999986533333
No 145
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.09 E-value=1.5 Score=33.62 Aligned_cols=48 Identities=23% Similarity=0.520 Sum_probs=32.3
Q ss_pred cccccccccccC---------C-ceec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 118 MCDICMEEVAGD---------K-ATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 118 ~C~IC~e~~~~~---------~-~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
+|+||--.|... + +..+ .|.|.|-.-|+.+++...-++| .||. |...+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~-----~CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG-----QCPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc-----cCCc--chhee
Confidence 677776665422 2 1222 6899999999999998765444 5888 76543
No 146
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.87 E-value=5 Score=46.63 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=5.5
Q ss_pred cCCCCCCCCc
Q 011726 277 KPCPKCHKPV 286 (478)
Q Consensus 277 k~CP~C~~~I 286 (478)
..||+|+..+
T Consensus 668 rkCPkCG~~t 677 (1337)
T PRK14714 668 RRCPSCGTET 677 (1337)
T ss_pred EECCCCCCcc
Confidence 4566665544
No 147
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.65 E-value=4.6 Score=39.33 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=14.4
Q ss_pred CceEe-ccccceecccc
Q 011726 293 NLVSC-ICGQAFCWLCG 308 (478)
Q Consensus 293 nhm~C-~C~~~FCw~C~ 308 (478)
.+++| .|+...|+.|.
T Consensus 96 ~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 96 LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred ceEEecccccccCCCCC
Confidence 56999 69999999998
No 148
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=62.35 E-value=3.3 Score=33.53 Aligned_cols=33 Identities=18% Similarity=0.473 Sum_probs=25.9
Q ss_pred CccccccccccccccccCCceecCCCCccchhh
Q 011726 112 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144 (478)
Q Consensus 112 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 144 (478)
.....|+|.-||-....+++..-.=|+.+|++|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 345789999999887666665555689999998
No 149
>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=61.88 E-value=2.1 Score=42.14 Aligned_cols=29 Identities=28% Similarity=0.535 Sum_probs=21.7
Q ss_pred CcCCCCCCCCccc-cCCCCceEe-cccccee
Q 011726 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAFC 304 (478)
Q Consensus 276 ~k~CP~C~~~IeK-~~GCnhm~C-~C~~~FC 304 (478)
|.+||+|+..|-+ .-.=|.+.| .|+++|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 5889999988875 344566889 5998863
No 150
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.75 E-value=3.2 Score=40.20 Aligned_cols=28 Identities=32% Similarity=0.911 Sum_probs=22.9
Q ss_pred cccccccccccccCCceecCCCCc-cchhhH
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCW 145 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~ 145 (478)
..-|.||++. +.+.+.|+|||. -|..|=
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhc
Confidence 5789999997 367889999995 788883
No 151
>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=61.49 E-value=5.5 Score=32.75 Aligned_cols=24 Identities=38% Similarity=0.890 Sum_probs=17.6
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~ 302 (478)
+.||+|+.++...+| .+.| .|++.
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 152
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=61.21 E-value=9.1 Score=26.62 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=22.9
Q ss_pred ccccccccccCCceecCCC--C---ccchhhHHHHHHH
Q 011726 119 CDICMEEVAGDKATKMDCG--H---CFCNDCWTEHFIV 151 (478)
Q Consensus 119 C~IC~e~~~~~~~~~l~Cg--H---~fC~~C~~~yi~~ 151 (478)
|-||++....+.+...+|+ - ....+|+..|+..
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 7799998655554555665 2 6788999999987
No 153
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.18 E-value=5.8 Score=44.12 Aligned_cols=35 Identities=29% Similarity=0.805 Sum_probs=28.9
Q ss_pred CcCCCCCCCCccccCCCCceEe-ccccc-----eecccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 310 (478)
+-.||+|..+..-..+=|.|.| .||++ .|..|++.
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 3589999988876666699999 59987 89999987
No 154
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=61.12 E-value=6.4 Score=27.67 Aligned_cols=26 Identities=35% Similarity=0.882 Sum_probs=16.9
Q ss_pred cCCCCCCCCceEEeccccc-eeeEec-CCcc
Q 011726 209 WCPSTPHCGNAIRVEEVEV-CEVECA-CGAQ 237 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~-~~v~C~-C~~~ 237 (478)
+|| .||..+....... ....|+ ||+.
T Consensus 2 FCp---~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP---KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC---CCCCccccccCCCCCEEECCcCCCe
Confidence 688 7999887664322 346676 7754
No 155
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=61.02 E-value=0.97 Score=35.36 Aligned_cols=47 Identities=32% Similarity=0.391 Sum_probs=34.2
Q ss_pred eCHHHHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 42 ITRESLLAAQKEDLRRVMELLSL---REHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 42 l~~~~i~~~~~~~i~~v~~~l~i---~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
||+++-.+ +..-+..|.++||= +.....-.|.+|.+++++.+..+..
T Consensus 20 Ls~ed~~~-L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 20 LSPEDQAQ-LYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp -TCHHHHH-HCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCHHHHHH-HHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 45555443 77788899999974 5566778888999999999888774
No 156
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.37 E-value=5.4 Score=44.67 Aligned_cols=51 Identities=20% Similarity=0.430 Sum_probs=36.2
Q ss_pred cccccccccccccc---CCce--ecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccC
Q 011726 115 STVMCDICMEEVAG---DKAT--KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (478)
Q Consensus 115 ~~~~C~IC~e~~~~---~~~~--~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~ 173 (478)
...+|+||+..+.. .-|. ...|.|.|...|+-.|+... | .-+||. |...++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss---~---~s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS---A---RSNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc---C---CCCCCc--cccccc
Confidence 45689999988652 1121 22689999999999999873 2 358998 776543
No 157
>PF12773 DZR: Double zinc ribbon
Probab=60.24 E-value=4.1 Score=28.51 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=7.4
Q ss_pred cCCCCCCCCccc
Q 011726 277 KPCPKCHKPVEK 288 (478)
Q Consensus 277 k~CP~C~~~IeK 288 (478)
+.||+|+..+..
T Consensus 30 ~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 30 KICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCCcC
Confidence 567777666553
No 158
>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=60.02 E-value=6.9 Score=41.91 Aligned_cols=34 Identities=26% Similarity=0.677 Sum_probs=22.5
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccc-----eecccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 310 (478)
-.||+|..+..--..=|.+.| .||+. .|..|++.
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 477788776653223346888 48866 68888765
No 159
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=59.53 E-value=4.1 Score=39.77 Aligned_cols=53 Identities=26% Similarity=0.611 Sum_probs=38.3
Q ss_pred CCCcccCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCC
Q 011726 204 NKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCH 283 (478)
Q Consensus 204 ~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~ 283 (478)
++.+-+|- .|+..|.+-+.- =+|.+.||..|... |. .|.||.|.
T Consensus 87 ~p~VHfCd---~Cd~PI~IYGRm-----IPCkHvFCl~CAr~-~~---------------------------dK~Cp~C~ 130 (389)
T KOG2932|consen 87 GPRVHFCD---RCDFPIAIYGRM-----IPCKHVFCLECARS-DS---------------------------DKICPLCD 130 (389)
T ss_pred CcceEeec---ccCCcceeeecc-----cccchhhhhhhhhc-Cc---------------------------cccCcCcc
Confidence 44566776 799887754321 15999999999753 21 18999999
Q ss_pred CCccccCCC
Q 011726 284 KPVEKNGGC 292 (478)
Q Consensus 284 ~~IeK~~GC 292 (478)
-.|+|..-|
T Consensus 131 d~VqrIeq~ 139 (389)
T KOG2932|consen 131 DRVQRIEQI 139 (389)
T ss_pred cHHHHHHHh
Confidence 999987665
No 160
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=58.52 E-value=7.3 Score=30.78 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=21.5
Q ss_pred CcCCCCCCCCccccCCCCceEe-ccccce
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
-..||.|+...-|..+=---.| +||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3689999999888777666677 477766
No 161
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=57.58 E-value=6.2 Score=33.86 Aligned_cols=24 Identities=46% Similarity=1.148 Sum_probs=18.8
Q ss_pred CcCCCCCCCCccccCCCCceEeccccceecccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCG 308 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~ 308 (478)
.+.||.|+.|..+. -|.-||.+|+
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 37999999998754 4477888887
No 162
>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=57.22 E-value=6.6 Score=27.36 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=17.5
Q ss_pred CcCCC--CCCCCccccCCCCceEe-cccc
Q 011726 276 TKPCP--KCHKPVEKNGGCNLVSC-ICGQ 301 (478)
Q Consensus 276 ~k~CP--~C~~~IeK~~GCnhm~C-~C~~ 301 (478)
-+.|| .|+.-|--..--+..+| +||+
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 37899 99987754444567888 7875
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=56.63 E-value=20 Score=30.29 Aligned_cols=42 Identities=24% Similarity=0.592 Sum_probs=28.7
Q ss_pred CCcCCCCCCCCccccCCCCceEe-ccccceeccccccccCCCCc
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTW 317 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~~ 317 (478)
+.+.|..|+.+.-..++.. ..| .|++.+|-.|+........|
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 5679999998766554444 789 59999999999873333333
No 164
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.60 E-value=3.6 Score=44.00 Aligned_cols=35 Identities=26% Similarity=0.738 Sum_probs=27.8
Q ss_pred ccccccccccccc--CCceecCCCCccchhhHHHHHH
Q 011726 116 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFI 150 (478)
Q Consensus 116 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~ 150 (478)
-..|+||+..|-. -.++++.|||..|+-|+.....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 3579999887543 3578899999999999987654
No 165
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.59 E-value=5.9 Score=44.17 Aligned_cols=38 Identities=29% Similarity=0.629 Sum_probs=30.9
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVK 152 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~ 152 (478)
..-.|.+|.-.+-...++..+|||.|..+|+...+..-
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHcc
Confidence 45689999988765656666999999999999887653
No 166
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=56.42 E-value=3.6 Score=39.72 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=23.6
Q ss_pred CcCCCCCCCCcc-ccCCCCceEe-ccccceec
Q 011726 276 TKPCPKCHKPVE-KNGGCNLVSC-ICGQAFCW 305 (478)
Q Consensus 276 ~k~CP~C~~~Ie-K~~GCnhm~C-~C~~~FCw 305 (478)
|.+||.|+..+- |.-+=|...| +|+|+|=-
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccccc
Confidence 579999998886 4667788888 59988743
No 167
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=55.99 E-value=3.9 Score=44.78 Aligned_cols=41 Identities=12% Similarity=0.147 Sum_probs=24.5
Q ss_pred cccccccccccccc--CCceec---CCCCccchhhHHHHHHHHHhc
Q 011726 115 STVMCDICMEEVAG--DKATKM---DCGHCFCNDCWTEHFIVKINE 155 (478)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l---~CgH~fC~~C~~~yi~~~i~~ 155 (478)
...+|.+|..+++. +-.-.+ .|+|.+|..||..+...-+..
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~ 140 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEES 140 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhcc
Confidence 34556666555432 112223 488888888888887765543
No 168
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.82 E-value=10 Score=24.51 Aligned_cols=27 Identities=33% Similarity=0.872 Sum_probs=13.5
Q ss_pred ccCCCCCCCCceEEe---ccccceeeEec-CCcc
Q 011726 208 KWCPSTPHCGNAIRV---EEVEVCEVECA-CGAQ 237 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~---~~~~~~~v~C~-C~~~ 237 (478)
++|| .|+..+.. .++......|+ ||..
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 33555567886 8764
No 169
>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=54.71 E-value=5.7 Score=34.74 Aligned_cols=10 Identities=30% Similarity=0.571 Sum_probs=5.3
Q ss_pred cccccccccc
Q 011726 115 STVMCDICME 124 (478)
Q Consensus 115 ~~~~C~IC~e 124 (478)
+..+|||=-+
T Consensus 125 eEg~CPIVIe 134 (167)
T PF05320_consen 125 EEGTCPIVIE 134 (167)
T ss_pred hcCCCcEEEe
Confidence 3456666544
No 170
>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=54.44 E-value=8.4 Score=31.76 Aligned_cols=26 Identities=31% Similarity=0.824 Sum_probs=16.8
Q ss_pred cCCCCCCCCccccCCCCceEec-cccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~-C~~~F 303 (478)
-+||+|+.-.-=..|=+ +.|. |+|+|
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCe-eECccccccc
Confidence 58999998766555533 5553 55554
No 171
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.13 E-value=14 Score=33.11 Aligned_cols=57 Identities=25% Similarity=0.453 Sum_probs=38.6
Q ss_pred cccccccccccc-ccCC----ceecCCCCccchhhHHHHHHHHHhcCCcccc---cCCCcccCCccC
Q 011726 115 STVMCDICMEEV-AGDK----ATKMDCGHCFCNDCWTEHFIVKINEGQSKRI---RCMAHKCNAICD 173 (478)
Q Consensus 115 ~~~~C~IC~e~~-~~~~----~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i---~CP~~~C~~~~~ 173 (478)
....|.||+--. ..+. .-...||..|..-|+..|+..-+...+++.| .||- |..++.
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 456788887531 1111 1234799999999999999987776665544 5887 776654
No 172
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.01 E-value=11 Score=36.02 Aligned_cols=53 Identities=17% Similarity=0.370 Sum_probs=38.2
Q ss_pred ccccccccccccccCCcee---cCCC-----CccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 115 STVMCDICMEEVAGDKATK---MDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~---l~Cg-----H~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..-.|=|||.+-. ++... -||. |.....|+..||..+-..+...++.||+ |..
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 4578999998743 22222 2554 6789999999999887644457899999 875
No 173
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.97 E-value=3.7 Score=39.30 Aligned_cols=30 Identities=33% Similarity=0.597 Sum_probs=23.4
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccceecccccc-cc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGA-TG 312 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~-~~ 312 (478)
.+|+-|--..+. -.| .|||-|||.|+-. |.
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t 247 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWT 247 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHHHHH
Confidence 679988877764 567 4999999999876 53
No 174
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=53.94 E-value=2.5 Score=29.54 Aligned_cols=34 Identities=29% Similarity=0.773 Sum_probs=27.7
Q ss_pred ccccccccccccccCCceec-CCCCccchhhHHHH
Q 011726 115 STVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEH 148 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~y 148 (478)
..++|..|-+.+|....... -||-.-|.+||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 46899999999877665554 79999999999864
No 175
>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=52.27 E-value=20 Score=25.43 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 53 EDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 53 ~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
+.|..++...|+++.-+...|...+||-++.+..|..
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 5688999999999999999999999999999988875
No 176
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=52.22 E-value=3.5 Score=40.17 Aligned_cols=89 Identities=25% Similarity=0.499 Sum_probs=47.5
Q ss_pred CCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHHHHhcCCCchHHHHHHHHH-HHHHHhhC----CCcccCC
Q 011726 137 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIEDN----KMVKWCP 211 (478)
Q Consensus 137 gH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~~~~-~~~~v~~~----~~~~~CP 211 (478)
|-++|..|-..-. ..||.||. |... -+++ ..+.+.|.-+. ++.+++.. +....|-
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 26788887 6532 2333 33444454332 33444432 2334454
Q ss_pred CCCCCCceEEecc-------ccceeeEec-CCccccccccCCCCC
Q 011726 212 STPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (478)
Q Consensus 212 ~~p~C~~~i~~~~-------~~~~~v~C~-C~~~fC~~C~~~~H~ 248 (478)
.|+..+.... .......|. |...||..|..-.|.
T Consensus 367 ---~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 367 ---VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ---eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 4665544322 123347897 999999999765553
No 177
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=52.01 E-value=7.1 Score=30.14 Aligned_cols=54 Identities=22% Similarity=0.633 Sum_probs=20.5
Q ss_pred CCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCC
Q 011726 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (478)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 293 (478)
-|+--|.........|-|. |+...|..|.. +. ++...+.||.|+.+..+..|+-
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 6887777766666778897 99888887743 11 1234589999999988777764
No 178
>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=51.98 E-value=8.9 Score=28.76 Aligned_cols=37 Identities=22% Similarity=0.536 Sum_probs=18.7
Q ss_pred ccccccccccccccccCCc-eec-CCCCccchhhHHHHH
Q 011726 113 LSSTVMCDICMEEVAGDKA-TKM-DCGHCFCNDCWTEHF 149 (478)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~-~~l-~CgH~fC~~C~~~yi 149 (478)
..+...|.+|...|..... ... .||+.||.+|....+
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 3456789999999854221 222 799999999986544
No 179
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=51.76 E-value=6 Score=38.30 Aligned_cols=32 Identities=28% Similarity=0.744 Sum_probs=25.7
Q ss_pred cCCCCCCCCccccCCCCceEe--ccccceeccccccccCCC
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGATGRDH 315 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C--~C~~~FCw~C~~~~~~~H 315 (478)
-+|--|.-.|- +-| .|||.||++|-..+-..|
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 180
>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=51.57 E-value=12 Score=23.05 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=12.9
Q ss_pred CCCCCCCCccccCCCCceEe
Q 011726 278 PCPKCHKPVEKNGGCNLVSC 297 (478)
Q Consensus 278 ~CP~C~~~IeK~~GCnhm~C 297 (478)
.||.|+..+.+..|=-+++|
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 49999999998888667776
No 181
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=51.54 E-value=13 Score=36.31 Aligned_cols=46 Identities=28% Similarity=0.617 Sum_probs=35.4
Q ss_pred cccccccccccccc--CCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 115 STVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
....||||.+.+.. ..+..++|||..-..|++.++.. . .+||. |..
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 45669999998532 34556799999999999998764 2 78998 877
No 182
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=51.18 E-value=11 Score=38.88 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=9.7
Q ss_pred CCCCCcccccccccc
Q 011726 108 DPMLPLSSTVMCDIC 122 (478)
Q Consensus 108 ~~~~~~~~~~~C~IC 122 (478)
.+.+|.+..|.|+-=
T Consensus 186 tP~LPDSTDFVCGTL 200 (458)
T PF10446_consen 186 TPELPDSTDFVCGTL 200 (458)
T ss_pred CCCCCCcccccCCCc
Confidence 355566777877753
No 183
>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=51.01 E-value=9.2 Score=32.54 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=17.3
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
+.||+|++..---.- +-++| +||..|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 679999987653222 56777 477653
No 184
>PRK14873 primosome assembly protein PriA; Provisional
Probab=50.93 E-value=11 Score=41.93 Aligned_cols=34 Identities=29% Similarity=0.712 Sum_probs=21.4
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccc----eecccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA----FCWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~----FCw~C~~~ 310 (478)
-.||+|..+..-..+=+.+.| .||+. .|-.|++.
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 477777776664444456788 48763 46666654
No 185
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=50.26 E-value=13 Score=27.68 Aligned_cols=14 Identities=43% Similarity=0.949 Sum_probs=10.9
Q ss_pred CCcCCCCCCCCccc
Q 011726 275 HTKPCPKCHKPVEK 288 (478)
Q Consensus 275 ~~k~CP~C~~~IeK 288 (478)
+.|+||.|+..+..
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 45999999976654
No 186
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.15 E-value=8.1 Score=38.73 Aligned_cols=42 Identities=26% Similarity=0.651 Sum_probs=28.8
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
....|.||.+.. .+...++|||.-| |.--+- ..+.||. |...
T Consensus 304 ~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~r 345 (355)
T KOG1571|consen 304 QPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCSK---------HLPQCPV--CRQR 345 (355)
T ss_pred CCCceEEecCCc--cceeeecCCcEEE--chHHHh---------hCCCCch--hHHH
Confidence 456899999984 4577889999866 543321 2356998 7653
No 187
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=49.87 E-value=13 Score=40.72 Aligned_cols=37 Identities=32% Similarity=0.528 Sum_probs=31.0
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHH
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIV 151 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~ 151 (478)
..+.|.||.-.+.....+...|+|....+|...|+..
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc
Confidence 4577999987776666677799999999999999986
No 188
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=49.71 E-value=8.8 Score=23.75 Aligned_cols=24 Identities=29% Similarity=0.778 Sum_probs=12.7
Q ss_pred cCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 277 KPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 277 k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
++||+|+.+|++ .+|=+...| +|.
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 445445555 453
No 189
>PRK05580 primosome assembly protein PriA; Validated
Probab=49.50 E-value=13 Score=41.56 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=23.4
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccc-----eecccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 310 (478)
-.||+|..+..--..=|.+.| .||+. .|..|++.
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 478888877653223356888 48876 58888765
No 190
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.19 E-value=10 Score=42.14 Aligned_cols=40 Identities=20% Similarity=0.571 Sum_probs=30.6
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..|..|--++. -+++...|||.|...|+. ++ .-.||. |..
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 57999977753 355677999999999998 33 368987 765
No 191
>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=49.17 E-value=75 Score=23.64 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 49 AAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 49 ~~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
..|.+.|..++...|++..-+..+|...+||.++.+..|.+
T Consensus 10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34667789999999999999999999999999998887764
No 192
>PF14149 YhfH: YhfH-like protein
Probab=48.32 E-value=1.5 Score=28.80 Aligned_cols=26 Identities=31% Similarity=0.790 Sum_probs=20.5
Q ss_pred hCCcCCCCCCCCccccCCCCceEe-cc
Q 011726 274 VHTKPCPKCHKPVEKNGGCNLVSC-IC 299 (478)
Q Consensus 274 ~~~k~CP~C~~~IeK~~GCnhm~C-~C 299 (478)
...|.||.||..|+--.-|-.++| +|
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 346999999999988777777777 45
No 193
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=48.00 E-value=20 Score=26.86 Aligned_cols=31 Identities=32% Similarity=0.623 Sum_probs=24.1
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCcccccc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~ 241 (478)
..|| +|++.-..-+.....|+|. ||...+..
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 4798 8999877666666779997 99987754
No 194
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=47.73 E-value=15 Score=26.45 Aligned_cols=32 Identities=28% Similarity=0.858 Sum_probs=25.2
Q ss_pred cccccccccccc-cCCceec-CCCCccchhhHHH
Q 011726 116 TVMCDICMEEVA-GDKATKM-DCGHCFCNDCWTE 147 (478)
Q Consensus 116 ~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~C~~~ 147 (478)
...|++|-+.+. .++.+.. .||-.|.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999984 3555555 8999999999965
No 195
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.34 E-value=15 Score=34.82 Aligned_cols=37 Identities=14% Similarity=0.223 Sum_probs=30.7
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhc
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE 155 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~ 155 (478)
-.|+.|+.++ .+++..+=||.||+.|+-+||..+-++
T Consensus 44 dcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 44 DCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 4688898876 577888889999999999999887654
No 196
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.27 E-value=11 Score=38.31 Aligned_cols=6 Identities=33% Similarity=0.872 Sum_probs=3.3
Q ss_pred cccccc
Q 011726 121 ICMEEV 126 (478)
Q Consensus 121 IC~e~~ 126 (478)
||++.-
T Consensus 396 Ic~~ts 401 (514)
T KOG3130|consen 396 ICSDTS 401 (514)
T ss_pred ccccCC
Confidence 666553
No 197
>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=47.13 E-value=26 Score=38.66 Aligned_cols=41 Identities=22% Similarity=0.251 Sum_probs=26.0
Q ss_pred CceeeCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHH
Q 011726 38 STKVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEK 82 (478)
Q Consensus 38 ~~~vl~~~~i~~~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~ 82 (478)
+++.|++.++.+..++.-..-.+- .+.-..||++-+|..+.
T Consensus 412 pf~~l~ksq~~kl~k~q~k~y~de----~dyr~kl~~kkq~ke~~ 452 (763)
T TIGR00993 412 PFKPLTKAQMAKLSKEQRKAYLEE----YDYRVKLLQKKQWREEL 452 (763)
T ss_pred CCccccHHHHHHHhHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence 468888888877555443322222 23456788889998664
No 198
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=46.99 E-value=13 Score=30.41 Aligned_cols=27 Identities=26% Similarity=0.693 Sum_probs=15.0
Q ss_pred CcCCCCCCCCc---cccCCCCceEe-ccccc
Q 011726 276 TKPCPKCHKPV---EKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 276 ~k~CP~C~~~I---eK~~GCnhm~C-~C~~~ 302 (478)
.-.||+|+... ....|=-|..| .||+.
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 22224446666 36654
No 199
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=46.89 E-value=13 Score=31.29 Aligned_cols=27 Identities=26% Similarity=0.594 Sum_probs=18.3
Q ss_pred cCCCCCCCCccc--cCCCCceEe-ccccce
Q 011726 277 KPCPKCHKPVEK--NGGCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK--~~GCnhm~C-~C~~~F 303 (478)
+.||+|+.++.- .++=+-+.| +||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 689999987764 112226888 488765
No 200
>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=46.72 E-value=15 Score=27.36 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=13.2
Q ss_pred ccchhhHHHHHHHHHhcC
Q 011726 139 CFCNDCWTEHFIVKINEG 156 (478)
Q Consensus 139 ~fC~~C~~~yi~~~i~~g 156 (478)
-||++|+..|+..+-.+.
T Consensus 11 gFCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEER 28 (68)
T ss_dssp S--HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 499999999999887654
No 201
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=46.54 E-value=16 Score=31.36 Aligned_cols=51 Identities=25% Similarity=0.531 Sum_probs=37.8
Q ss_pred ccccccccccccccCCceec--CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVAGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
.-.+|.||-+......+... -||=..|.-|....|...- ....||. |+..+
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 46899999998543332222 4899999999999998743 3578999 88765
No 202
>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=45.81 E-value=14 Score=26.59 Aligned_cols=44 Identities=23% Similarity=0.544 Sum_probs=30.8
Q ss_pred ccccccccccccCCceecCCC--CccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 117 VMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
..|..|-.+++.+.....-|. ..||.+|....+. -.||. |+..+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGel 51 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN----------GVCPN--CGGEL 51 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc----------CcCcC--CCCcc
Confidence 468888888876654444555 4799999887653 26888 77644
No 203
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=45.59 E-value=12 Score=38.71 Aligned_cols=6 Identities=0% Similarity=-0.009 Sum_probs=2.5
Q ss_pred HHHHHH
Q 011726 346 YMHYHN 351 (478)
Q Consensus 346 y~~y~~ 351 (478)
|..|+.
T Consensus 407 ~rk~C~ 412 (458)
T PF10446_consen 407 WRKHCR 412 (458)
T ss_pred HHHHHH
Confidence 344443
No 204
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=45.40 E-value=4.7 Score=29.36 Aligned_cols=16 Identities=50% Similarity=0.835 Sum_probs=8.5
Q ss_pred CcCCCCCCCCccccCC
Q 011726 276 TKPCPKCHKPVEKNGG 291 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~G 291 (478)
+..||.|+++++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 3689999999986433
No 205
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.97 E-value=15 Score=41.86 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=24.1
Q ss_pred hCCcCCCCCCCCccccCCCCceEec-ccc-----ceecccccc
Q 011726 274 VHTKPCPKCHKPVEKNGGCNLVSCI-CGQ-----AFCWLCGGA 310 (478)
Q Consensus 274 ~~~k~CP~C~~~IeK~~GCnhm~C~-C~~-----~FCw~C~~~ 310 (478)
...+.||.|+... ....|. ||. .||-.|+..
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 4568999999885 347894 985 499999766
No 206
>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=44.89 E-value=30 Score=30.86 Aligned_cols=32 Identities=28% Similarity=0.530 Sum_probs=20.0
Q ss_pred hCCCcccCCCCCCCCceEEeccccceeeEec-CCcc
Q 011726 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (478)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 237 (478)
.++.+-.|| .|+.-+...+.-...+.|| ||..
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 345666898 5886666555333457777 7765
No 207
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=44.51 E-value=25 Score=24.79 Aligned_cols=47 Identities=17% Similarity=0.436 Sum_probs=23.9
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..|+|-+..+. .......|.|.-|.| +..|+....+.+. .+||. |..
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 56888877652 233445999998854 7788887765544 78998 753
No 208
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=44.51 E-value=23 Score=28.66 Aligned_cols=28 Identities=39% Similarity=0.850 Sum_probs=18.2
Q ss_pred ccCCCCCCCCceEEeccccc-eeeEec-CCccc
Q 011726 208 KWCPSTPHCGNAIRVEEVEV-CEVECA-CGAQF 238 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-C~~~f 238 (478)
.+|| .|++.+.++.+.. ..+.|+ |++.+
T Consensus 2 ~FCP---~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP---TCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccC---CCCCEEEEecCCeEeeEEcCCCCcee
Confidence 4798 7999998876443 445554 55543
No 209
>PRK10220 hypothetical protein; Provisional
Probab=44.46 E-value=15 Score=30.27 Aligned_cols=26 Identities=23% Similarity=0.700 Sum_probs=15.9
Q ss_pred cCCCCCCCCccccCCCCceEec-cccce
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~-C~~~F 303 (478)
-.||+|..-.-=..|= .+.|. |+|+|
T Consensus 4 P~CP~C~seytY~d~~-~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECCcccCcC
Confidence 5899999766655553 24552 55543
No 210
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=43.39 E-value=17 Score=25.78 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=23.6
Q ss_pred cccccccccccCCceecCCCCccchhhHHHH
Q 011726 118 MCDICMEEVAGDKATKMDCGHCFCNDCWTEH 148 (478)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 148 (478)
.|+||...+..-..+.+.=| ..|.+|+...
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 49999998765444667778 8999999876
No 211
>PRK12495 hypothetical protein; Provisional
Probab=43.21 E-value=29 Score=32.48 Aligned_cols=27 Identities=26% Similarity=0.720 Sum_probs=20.0
Q ss_pred CCcCCCCCCCCccccCCCCceEeccccceecccccc
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 310 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~ 310 (478)
..+.||.|+.||-+..|| .||-.|...
T Consensus 41 sa~hC~~CG~PIpa~pG~---------~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ---------EFCPTCQQP 67 (226)
T ss_pred chhhcccccCcccCCCCe---------eECCCCCCc
Confidence 358999999999987776 455566544
No 212
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.80 E-value=15 Score=35.81 Aligned_cols=22 Identities=45% Similarity=1.091 Sum_probs=16.0
Q ss_pred CcCCCCCCCCccc--cCCCCceEe
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC 297 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C 297 (478)
.++||.|+.+|++ .+|=.-.+|
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~C 258 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFC 258 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEEC
Confidence 3799999999986 566444444
No 213
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.64 E-value=15 Score=35.83 Aligned_cols=25 Identities=40% Similarity=1.060 Sum_probs=20.2
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
-++|+.|+.+|+| -+|=+-.+| .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4799999999997 578777777 475
No 214
>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=42.50 E-value=4.6e+02 Score=29.57 Aligned_cols=30 Identities=17% Similarity=0.289 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCC
Q 011726 433 QHLFEDQQQQLEANVEKLSKFLEEPFDQYP 462 (478)
Q Consensus 433 ~~~fe~~q~~le~~~e~L~~~le~~~~~~~ 462 (478)
.+-..+.|+.|.++++.+...+......++
T Consensus 602 ~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS 631 (717)
T PF10168_consen 602 YEEAKDKQEKLMKRVDRVLQLLNSQLPVLS 631 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 345666677777777777777765444333
No 215
>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=42.46 E-value=11 Score=26.62 Aligned_cols=25 Identities=28% Similarity=0.647 Sum_probs=14.6
Q ss_pred cCCCCCCCCccccCCC--CceEe-cccc
Q 011726 277 KPCPKCHKPVEKNGGC--NLVSC-ICGQ 301 (478)
Q Consensus 277 k~CP~C~~~IeK~~GC--nhm~C-~C~~ 301 (478)
-+|++|+..+-+.++= -.|.| +||.
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 4677777776664332 24666 5664
No 216
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=42.44 E-value=54 Score=28.00 Aligned_cols=52 Identities=27% Similarity=0.383 Sum_probs=35.5
Q ss_pred HHHHHHHHhhhhhhcc-ceeeeeccCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 011726 392 NGLYRLFRSRRVLSYS-YPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEE 456 (478)
Q Consensus 392 ~a~~~l~~~r~~L~~s-y~~~yy~~~~~~~~~~~~~~~~~~~~~~fe~~q~~le~~~e~L~~~le~ 456 (478)
+-+.+|.+.|||||.- ||..-=. .+...+.-+|.....|...++.|..-+..
T Consensus 47 eEVvrlKQrRRTLKNRGYA~sCR~-------------KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~ 99 (135)
T KOG4196|consen 47 EEVVRLKQRRRTLKNRGYAQSCRV-------------KRVQQKHELEKEKAELQQQVEKLKEENSR 99 (135)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4466888999999983 3322111 23466777888888888888888776664
No 217
>smart00336 BBOX B-Box-type zinc finger.
Probab=42.29 E-value=23 Score=23.30 Aligned_cols=32 Identities=34% Similarity=0.785 Sum_probs=25.1
Q ss_pred cCCCCCC-CCccccCCCCceEe-ccccceeccccccccCCC
Q 011726 277 KPCPKCH-KPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (478)
Q Consensus 277 k~CP~C~-~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H 315 (478)
..|+.|. .++. ++| .|..-.|..|...-+.+|
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 5789997 7777 999 599999999986633334
No 218
>PHA02929 N1R/p28-like protein; Provisional
Probab=42.14 E-value=11 Score=36.04 Aligned_cols=38 Identities=24% Similarity=0.407 Sum_probs=26.4
Q ss_pred CcCCCCCCCCccccCCCC---ceEeccccceeccccccccC
Q 011726 276 TKPCPKCHKPVEKNGGCN---LVSCICGQAFCWLCGGATGR 313 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCn---hm~C~C~~~FCw~C~~~~~~ 313 (478)
...||-|.-.+.....-+ -+.-.|+|.||..|...|..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 468999998876543222 13346888999999988754
No 219
>PRK11827 hypothetical protein; Provisional
Probab=41.65 E-value=20 Score=26.41 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=17.2
Q ss_pred cCCCCCCCCccccCCCCceEe-cccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQ 301 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~ 301 (478)
-.||.|+.+.+-..+=+.+.| .||.
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 589999988876555455666 3553
No 220
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=41.54 E-value=16 Score=36.29 Aligned_cols=47 Identities=21% Similarity=0.592 Sum_probs=31.1
Q ss_pred cccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
.+...|.||...+. -...+||+|..|.-|--..-.-- ..-.||. |..
T Consensus 59 Een~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~RlRALY------~~K~C~~--CrT 105 (493)
T COG5236 59 EENMNCQICAGSTT--YSARYPCGHQICHACAVRLRALY------MQKGCPL--CRT 105 (493)
T ss_pred cccceeEEecCCce--EEEeccCCchHHHHHHHHHHHHH------hccCCCc--ccc
Confidence 35678999998753 33456999999999965432211 1236777 765
No 221
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=40.60 E-value=23 Score=22.69 Aligned_cols=12 Identities=33% Similarity=0.515 Sum_probs=8.6
Q ss_pred CcCCCCCCCCcc
Q 011726 276 TKPCPKCHKPVE 287 (478)
Q Consensus 276 ~k~CP~C~~~Ie 287 (478)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 368888887654
No 222
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=40.39 E-value=41 Score=26.09 Aligned_cols=48 Identities=23% Similarity=0.614 Sum_probs=20.5
Q ss_pred cccccccccccccc---CCceec--CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 115 STVMCDICMEEVAG---DKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 115 ~~~~C~IC~e~~~~---~~~~~l--~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
....|.||-+++.. .++|.. .|+-..|+.|+.- .+++|. -.||. |+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY----Erkeg~---q~Cpq--Ckt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY----ERKEGN---QVCPQ--CKTR 60 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH----HHHTS----SB-TT--T--B
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHH----HhhcCc---ccccc--cCCC
Confidence 45689999999653 244443 7899999999764 345665 47887 7643
No 223
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.27 E-value=17 Score=24.37 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=17.4
Q ss_pred CCCCCCCCccccCCCCceEeccccceeccccccc
Q 011726 278 PCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (478)
Q Consensus 278 ~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~ 311 (478)
.||+|+..++...- ..+. ..-|-.|++.|
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 59999987774322 1122 33456777776
No 224
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=40.17 E-value=17 Score=35.51 Aligned_cols=25 Identities=40% Similarity=1.024 Sum_probs=18.3
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
.++||.|+.+|+| .+|=.-.+| .|+
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 566555566 354
No 225
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.00 E-value=16 Score=27.64 Aligned_cols=44 Identities=25% Similarity=0.627 Sum_probs=30.6
Q ss_pred ccccccccccccCCceecCCC--CccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 117 VMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
..|..|-.+++++..-.+-|. |.||.+|...-+. | .||. |+..+
T Consensus 6 PnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-----g-----~CPn--CGGel 51 (84)
T COG3813 6 PNCECCDRDLPPDSTDARICTFECTFCADCAENRLH-----G-----LCPN--CGGEL 51 (84)
T ss_pred CCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-----C-----cCCC--CCchh
Confidence 358888778876655555564 8899999876543 2 5887 77644
No 226
>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=39.81 E-value=18 Score=35.39 Aligned_cols=25 Identities=40% Similarity=0.958 Sum_probs=18.1
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
.++||.|+.+|.+ .+|=.-.+| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 3699999999986 566555556 353
No 227
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.35 E-value=40 Score=30.75 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=14.3
Q ss_pred HHHHHHHHcCCCHHHHHHHH
Q 011726 54 DLRRVMELLSLREHHARTLL 73 (478)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~lL 73 (478)
...++++.|||+...++-+|
T Consensus 38 tdeeLA~~Lgi~~~~VRk~L 57 (178)
T PRK06266 38 TDEEIAEQTGIKLNTVRKIL 57 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 44667777788777777766
No 228
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=39.33 E-value=43 Score=29.43 Aligned_cols=19 Identities=26% Similarity=0.560 Sum_probs=14.3
Q ss_pred HHHHHHcCCCHHHHHHHHH
Q 011726 56 RRVMELLSLREHHARTLLI 74 (478)
Q Consensus 56 ~~v~~~l~i~~~~a~~lL~ 74 (478)
.++++.|||+....+.+|.
T Consensus 19 edLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 19 EDLAELLGIKQKQLRKILY 37 (147)
T ss_pred HHHHHHhCCCHHHHHHHHH
Confidence 4667778888888877773
No 229
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.24 E-value=18 Score=35.38 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=18.3
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
.++||+|+.+|++ .+|=.-.+| .|+
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 230
>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=39.23 E-value=17 Score=24.79 Aligned_cols=41 Identities=24% Similarity=0.601 Sum_probs=19.4
Q ss_pred ccccccccccCCce-ecCCCCccchhhHHHHHHHHHhcCCcccccCCC
Q 011726 119 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (478)
Q Consensus 119 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~ 165 (478)
|.+|-+.+.....- ...|+-.+...|+..|+...- ..+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 66777665322211 125888999999999998631 127886
No 231
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.93 E-value=19 Score=35.47 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=19.0
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
-++||.|+.+|.| .+|=.-.+| .|+
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 577666666 464
No 232
>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=38.92 E-value=30 Score=24.93 Aligned_cols=27 Identities=41% Similarity=0.815 Sum_probs=20.0
Q ss_pred cCCCCCCCCceEEecc-ccceeeEec-CCccc
Q 011726 209 WCPSTPHCGNAIRVEE-VEVCEVECA-CGAQF 238 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~-~~~~~v~C~-C~~~f 238 (478)
-|| .|+.-|.+.+ ...-.+.|+ ||..+
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 7999998765 234568897 98875
No 233
>PRK10445 endonuclease VIII; Provisional
Probab=38.56 E-value=19 Score=35.05 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=18.7
Q ss_pred CcCCCCCCCCccc--cCCCCceEe-ccc
Q 011726 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (478)
Q Consensus 276 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 300 (478)
-++||.|+.+|++ .+|=.-.+| .|+
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 577655666 364
No 234
>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=38.31 E-value=65 Score=36.63 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 011726 68 HARTLLIHYRWDVEKLLAVL 87 (478)
Q Consensus 68 ~a~~lL~~~~W~~e~l~e~~ 87 (478)
.++..+++|+-.+=.|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 46666667766666666655
No 235
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.06 E-value=12 Score=39.21 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=19.8
Q ss_pred CcCCCCCCCCccccCCCCceEe--ccccceecccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGA 310 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C--~C~~~FCw~C~~~ 310 (478)
-..||-|-.+-. .-+ .|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 479999987655 334 2888888888654
No 236
>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=37.82 E-value=21 Score=33.90 Aligned_cols=21 Identities=29% Similarity=0.765 Sum_probs=11.5
Q ss_pred HHHHHHHhCCcCCCCCCCC-ccc
Q 011726 267 ETVNWITVHTKPCPKCHKP-VEK 288 (478)
Q Consensus 267 ~~~~~i~~~~k~CP~C~~~-IeK 288 (478)
.+..|+..|. .||+|+.. +.+
T Consensus 23 ltE~Wv~~n~-yCP~Cg~~~L~~ 44 (254)
T PF06044_consen 23 LTEDWVAENM-YCPNCGSKPLSK 44 (254)
T ss_dssp HHHHHHHHH----TTT--SS-EE
T ss_pred HHHHHHHHCC-cCCCCCChhHhh
Confidence 4668888775 89999987 654
No 237
>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=36.79 E-value=34 Score=23.03 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=7.9
Q ss_pred cCCCCCCC-Cccc
Q 011726 277 KPCPKCHK-PVEK 288 (478)
Q Consensus 277 k~CP~C~~-~IeK 288 (478)
..||.|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 57777776 5544
No 238
>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=36.68 E-value=1.5e+02 Score=24.22 Aligned_cols=47 Identities=26% Similarity=0.290 Sum_probs=37.1
Q ss_pred eCHHHHHH-----HHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 011726 42 ITRESLLA-----AQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (478)
Q Consensus 42 l~~~~i~~-----~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~ 89 (478)
.+|++|+. .++++|-.+++-+.++...|.+||. ..=-.+.|++.|..
T Consensus 24 qpPeeIl~~AYEy~VkeDi~m~~ee~~l~~~qa~ALl~-sp~PL~~iY~~w~~ 75 (101)
T PF12959_consen 24 QPPEEILNHAYEYTVKEDILMAMEELELPDQQAKALLK-SPSPLADIYREWEK 75 (101)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHc-CCChHHHHHHHHHh
Confidence 46778876 4678889999999999999999994 44556778888874
No 239
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=36.48 E-value=26 Score=38.75 Aligned_cols=47 Identities=15% Similarity=0.352 Sum_probs=32.4
Q ss_pred cccccccccccccCCce-ecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 116 TVMCDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...|++|+..+...... ...|+|.||..|+..|-..+ -.||. |...+
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF 170 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEF 170 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhh
Confidence 35699999886432222 34899999999999986642 36877 55443
No 240
>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=36.44 E-value=33 Score=38.97 Aligned_cols=9 Identities=11% Similarity=0.014 Sum_probs=4.7
Q ss_pred HHHHHcCCC
Q 011726 57 RVMELLSLR 65 (478)
Q Consensus 57 ~v~~~l~i~ 65 (478)
++++.||.+
T Consensus 707 ~l~~aL~~~ 715 (784)
T PF04931_consen 707 ALAKALGDA 715 (784)
T ss_pred HHHHHhccc
Confidence 455556643
No 241
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.14 E-value=26 Score=24.03 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=5.4
Q ss_pred cCCCCCCCCc
Q 011726 277 KPCPKCHKPV 286 (478)
Q Consensus 277 k~CP~C~~~I 286 (478)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 4566655544
No 242
>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=36.05 E-value=24 Score=19.19 Aligned_cols=16 Identities=31% Similarity=0.793 Sum_probs=12.8
Q ss_pred ccccccCCCCCCCCcc
Q 011726 238 FCFSCLSEAHSPCSCS 253 (478)
Q Consensus 238 fC~~C~~~~H~~~~C~ 253 (478)
.|+.|+..-|....|.
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 5899999999876664
No 243
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=35.71 E-value=32 Score=33.93 Aligned_cols=51 Identities=18% Similarity=0.483 Sum_probs=35.3
Q ss_pred ccccccccccccc-cCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
.-|.|||=-+... .+.++.|.|||.+=+.=+... -++|. ..++||- |+..-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~L----S~nG~-~~FKCPY--CP~~~ 386 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVL----SQNGV-LSFKCPY--CPEMS 386 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHH----hhcCc-EEeeCCC--CCcch
Confidence 4689998666533 356788899999877655543 24565 5889998 87643
No 244
>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=35.60 E-value=40 Score=29.96 Aligned_cols=37 Identities=27% Similarity=0.564 Sum_probs=24.0
Q ss_pred cccccccccccccCCceecCC-------CCccc------hhhHHHHHHHHHh
Q 011726 116 TVMCDICMEEVAGDKATKMDC-------GHCFC------NDCWTEHFIVKIN 154 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~C-------gH~fC------~~C~~~yi~~~i~ 154 (478)
..+||||++- +.+.+.|-| .-+.| .+|+.+|-....+
T Consensus 2 d~~CpICme~--PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~ 51 (162)
T PF07800_consen 2 DVTCPICMEH--PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGK 51 (162)
T ss_pred CccCceeccC--CCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcC
Confidence 4689999985 245555543 33444 5799988876543
No 245
>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=35.09 E-value=53 Score=23.95 Aligned_cols=30 Identities=17% Similarity=0.323 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChHHH
Q 011726 54 DLRRVMELLSLREHHARTLLIHYRWDVEKL 83 (478)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l 83 (478)
.+.+|++.||++......-...++|+...-
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~ 44 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLP 44 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCc
Confidence 468899999999999999999999996543
No 246
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=34.80 E-value=14 Score=29.22 Aligned_cols=35 Identities=29% Similarity=0.503 Sum_probs=28.1
Q ss_pred cCCCCCCCCccccCCCCceEeccccceeccccccccCC
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRD 314 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~ 314 (478)
..||.|+.| ...|--+.+.|++.|=..|...|-..
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 45677788889999999999998653
No 247
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.76 E-value=39 Score=24.76 Aligned_cols=31 Identities=32% Similarity=0.618 Sum_probs=22.4
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCcccccc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~ 241 (478)
..|| +|++...+-+.....|.|. ||...+.-
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 4688 8998877666555668896 88876543
No 248
>PLN02189 cellulose synthase
Probab=34.12 E-value=28 Score=40.05 Aligned_cols=59 Identities=29% Similarity=0.621 Sum_probs=42.0
Q ss_pred cCCCCCCCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCcc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 287 (478)
-|. -|+--+.........|-|. |+...|..|-.- . . +...+.||.|+....
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------R---------REGTQNCPQCKTRYK 87 (1040)
T ss_pred ccc---ccccccCcCCCCCEEEeeccCCCccccchhhh----------h------h---------hcCCccCcccCCchh
Confidence 565 6888877666666779998 999999998631 0 0 123378999999888
Q ss_pred ccCCCCce
Q 011726 288 KNGGCNLV 295 (478)
Q Consensus 288 K~~GCnhm 295 (478)
+--|++.+
T Consensus 88 r~kgs~~v 95 (1040)
T PLN02189 88 RLKGSPRV 95 (1040)
T ss_pred hccCCCCc
Confidence 66666553
No 249
>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=33.88 E-value=20 Score=31.51 Aligned_cols=95 Identities=15% Similarity=0.262 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhcCCCccCCCCCCC--Cccccccccccccc
Q 011726 48 LAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPML--PLSSTVMCDICMEE 125 (478)
Q Consensus 48 ~~~~~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~~~~~~~~~~~~~gl~~~~~~~~~~--~~~~~~~C~IC~e~ 125 (478)
...+.++|.+....+|+..-.. .+-..=-|+.|.+.+. ++ .-|.+.||.++....... .......||-|-..
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 3344444444333346543211 1122345888776553 22 346788998776431111 01224789999876
Q ss_pred cc--cCCceecCCC-CccchhhHHHH
Q 011726 126 VA--GDKATKMDCG-HCFCNDCWTEH 148 (478)
Q Consensus 126 ~~--~~~~~~l~Cg-H~fC~~C~~~y 148 (478)
.. .+.+-+..|. .++|.+|..-|
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 2344556887 67899997544
No 250
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.72 E-value=41 Score=32.89 Aligned_cols=34 Identities=21% Similarity=0.563 Sum_probs=23.3
Q ss_pred HHHHHhCCcCCCCCCCCccccCCCCceEe-ccccce
Q 011726 269 VNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 269 ~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
..|... -+-||+|+.+.+-..|=-.+.| .||+.+
T Consensus 105 ~~w~~~-~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 105 LEWYRS-HRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHhh-CcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 345443 3789999988887777666777 477554
No 251
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=33.67 E-value=19 Score=40.84 Aligned_cols=24 Identities=50% Similarity=1.297 Sum_probs=18.8
Q ss_pred cCCCCCCC-CccccCCCCceEe-ccccc
Q 011726 277 KPCPKCHK-PVEKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 277 k~CP~C~~-~IeK~~GCnhm~C-~C~~~ 302 (478)
-.||-|+. .|+..|||| || .||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999986 778899997 67 47654
No 252
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=33.48 E-value=26 Score=32.24 Aligned_cols=25 Identities=36% Similarity=0.844 Sum_probs=19.9
Q ss_pred CCCCCCCCccccCCCCceEe-ccccce
Q 011726 278 PCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 278 ~CP~C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
.||+|+.++.+ .+.|+|.| .||+..
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEE-CCCCEEECCCCCCEE
Confidence 79999999877 55599999 598643
No 253
>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=33.42 E-value=67 Score=22.78 Aligned_cols=46 Identities=20% Similarity=0.435 Sum_probs=24.5
Q ss_pred cccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCccCHHHHH
Q 011726 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (478)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (478)
.+.||.|...++.. =|..++...=... ...+.||. |...+....+.
T Consensus 2 ~f~CP~C~~~~~~~--------------~L~~H~~~~H~~~-~~~v~CPi--C~~~~~~~l~~ 47 (54)
T PF05605_consen 2 SFTCPYCGKGFSES--------------SLVEHCEDEHRSE-SKNVVCPI--CSSRVTDNLIR 47 (54)
T ss_pred CcCCCCCCCccCHH--------------HHHHHHHhHCcCC-CCCccCCC--chhhhhhHHHH
Confidence 57899998754311 1233333321111 24689998 87655443333
No 254
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=33.17 E-value=25 Score=40.80 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 011726 435 LFEDQQQQLEANVEKLSKFL 454 (478)
Q Consensus 435 ~fe~~q~~le~~~e~L~~~l 454 (478)
-||..|....+++|+|...-
T Consensus 2418 ~FEtKer~Fnka~EK~RnQh 2437 (3015)
T KOG0943|consen 2418 GFETKERKFNKAMEKLRNQH 2437 (3015)
T ss_pred ccchHHHHHHHHHHHHHhcc
Confidence 36666666666666665443
No 255
>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=32.69 E-value=22 Score=22.64 Aligned_cols=10 Identities=30% Similarity=1.006 Sum_probs=5.0
Q ss_pred cCCCCCCCCc
Q 011726 277 KPCPKCHKPV 286 (478)
Q Consensus 277 k~CP~C~~~I 286 (478)
-+||.|+..|
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 4566665544
No 256
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=32.50 E-value=11 Score=37.25 Aligned_cols=30 Identities=30% Similarity=0.903 Sum_probs=21.8
Q ss_pred cCCCCCCCCceEEeccccceeeEecCCcccccccc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCL 243 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~ 243 (478)
+|| -|-..+-..+.. .+-|+||+..|.-|-
T Consensus 16 ~cp---lcie~mditdkn--f~pc~cgy~ic~fc~ 45 (480)
T COG5175 16 YCP---LCIEPMDITDKN--FFPCPCGYQICQFCY 45 (480)
T ss_pred cCc---ccccccccccCC--cccCCcccHHHHHHH
Confidence 698 686655555543 368999999988884
No 257
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.19 E-value=38 Score=20.07 Aligned_cols=7 Identities=57% Similarity=1.630 Sum_probs=4.6
Q ss_pred cCCCCCC
Q 011726 277 KPCPKCH 283 (478)
Q Consensus 277 k~CP~C~ 283 (478)
-.||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4677776
No 258
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=31.74 E-value=18 Score=26.44 Aligned_cols=34 Identities=29% Similarity=0.698 Sum_probs=26.5
Q ss_pred cCCCCCCCCccc--cCCCCceEe-ccccceecccccc
Q 011726 277 KPCPKCHKPVEK--NGGCNLVSC-ICGQAFCWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK--~~GCnhm~C-~C~~~FCw~C~~~ 310 (478)
..||-|+...-- .+-=|+=+| .|+...|-+||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 579999987621 233589999 5999999999865
No 259
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=31.62 E-value=32 Score=25.08 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.6
Q ss_pred CCcCCCCCCCCcc
Q 011726 275 HTKPCPKCHKPVE 287 (478)
Q Consensus 275 ~~k~CP~C~~~Ie 287 (478)
+.-.||+|+.++.
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 4568999999887
No 260
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.38 E-value=24 Score=26.18 Aligned_cols=14 Identities=57% Similarity=1.054 Sum_probs=11.9
Q ss_pred CCcCCCCCCCCccc
Q 011726 275 HTKPCPKCHKPVEK 288 (478)
Q Consensus 275 ~~k~CP~C~~~IeK 288 (478)
.+.+||.|+++++.
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 35799999999985
No 261
>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=31.23 E-value=44 Score=22.50 Aligned_cols=26 Identities=38% Similarity=0.782 Sum_probs=14.0
Q ss_pred cCCCCCCCCceEEeccccceeeEec-CCcc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 237 (478)
.|| .|+.-....+...-.+.|+ ||..
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 487 6887554334333345665 6654
No 262
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.13 E-value=79 Score=26.36 Aligned_cols=37 Identities=27% Similarity=0.599 Sum_probs=23.6
Q ss_pred cccCCCCCCCCceEEeccccceeeEecCCccccccccCCCCCCCCcchhHHHHHHh
Q 011726 207 VKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKC 262 (478)
Q Consensus 207 ~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~ 262 (478)
...|+ +|+.... +.-+|+..+|..|+.. ....|..+.
T Consensus 42 ~~~C~---~Cg~~~~--------~~~SCk~R~CP~C~~~--------~~~~W~~~~ 78 (111)
T PF14319_consen 42 RYRCE---DCGHEKI--------VYNSCKNRHCPSCQAK--------ATEQWIEKQ 78 (111)
T ss_pred eeecC---CCCceEE--------ecCcccCcCCCCCCCh--------HHHHHHHHH
Confidence 34676 5876543 2225999999999864 455666543
No 263
>PHA02926 zinc finger-like protein; Provisional
Probab=30.95 E-value=21 Score=33.57 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=24.4
Q ss_pred CcCCCCCCCCc-cccC-CCCceEe---ccccceeccccccccCC
Q 011726 276 TKPCPKCHKPV-EKNG-GCNLVSC---ICGQAFCWLCGGATGRD 314 (478)
Q Consensus 276 ~k~CP~C~~~I-eK~~-GCnhm~C---~C~~~FCw~C~~~~~~~ 314 (478)
-+.|+-|--.+ +|.. ++. .+- .|+|-||+.|...|...
T Consensus 170 E~eCgICmE~I~eK~~~~eR-rFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDR-YFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred CCCCccCccccccccccccc-cccccCCCCchHHHHHHHHHHHh
Confidence 47899998665 4421 111 111 38888999999998654
No 264
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.95 E-value=30 Score=26.75 Aligned_cols=29 Identities=28% Similarity=0.518 Sum_probs=22.0
Q ss_pred cCCCCCCCCccccCCCCceEeccc--cceecccccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCICG--QAFCWLCGGATG 312 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~C~--~~FCw~C~~~~~ 312 (478)
..||.|++.+. |.=+=| ...|-.|.+.|-
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEee
Confidence 57999998877 555433 567999999974
No 265
>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=30.63 E-value=39 Score=24.78 Aligned_cols=27 Identities=33% Similarity=0.715 Sum_probs=18.9
Q ss_pred cCCCCCCCC----ccccCCCCceEe-ccccce
Q 011726 277 KPCPKCHKP----VEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 277 k~CP~C~~~----IeK~~GCnhm~C-~C~~~F 303 (478)
-.||+|+.+ +-+..|=.++.| .|||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 479999864 234566678899 598753
No 266
>PF14353 CpXC: CpXC protein
Probab=30.48 E-value=43 Score=28.51 Aligned_cols=11 Identities=45% Similarity=1.283 Sum_probs=8.0
Q ss_pred cCCCCCCCCceEEe
Q 011726 209 WCPSTPHCGNAIRV 222 (478)
Q Consensus 209 ~CP~~p~C~~~i~~ 222 (478)
.|| .|+..+..
T Consensus 3 tCP---~C~~~~~~ 13 (128)
T PF14353_consen 3 TCP---HCGHEFEF 13 (128)
T ss_pred CCC---CCCCeeEE
Confidence 587 69987664
No 267
>PF14353 CpXC: CpXC protein
Probab=30.40 E-value=21 Score=30.46 Aligned_cols=50 Identities=28% Similarity=0.606 Sum_probs=29.2
Q ss_pred ccCCCcccCCccCHHHHHHHhcCCCchHHHHHHHHHHHHHHhhCCCcccCCCCCCCCceEEec
Q 011726 161 IRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE 223 (478)
Q Consensus 161 i~CP~~~C~~~~~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~ 223 (478)
|+||. |+..+..+....+-...+|++.++ .+...-....|| .||..+...
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP---~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCP---SCGHKFRLE 51 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECC---CCCCceecC
Confidence 78998 888766554433333334544433 223333556898 799877654
No 268
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.16 E-value=18 Score=35.47 Aligned_cols=26 Identities=31% Similarity=0.863 Sum_probs=18.1
Q ss_pred CcCCCCCCCCccccCCCCceEe----ccccceecccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSC----ICGQAFCWLCGGA 310 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C----~C~~~FCw~C~~~ 310 (478)
.+.||-|.-. |.| .|+|.|||+|.+.
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 3678777533 344 2999999999764
No 269
>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=30.13 E-value=47 Score=24.03 Aligned_cols=33 Identities=27% Similarity=0.440 Sum_probs=20.1
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCcccccccc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCL 243 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~ 243 (478)
..|| +|++.-.+-+.....|.|. |+...|.-=+
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 4688 8998877666556679997 9998876433
No 270
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=30.01 E-value=27 Score=29.18 Aligned_cols=8 Identities=38% Similarity=1.377 Sum_probs=4.5
Q ss_pred cCCCCCCC
Q 011726 277 KPCPKCHK 284 (478)
Q Consensus 277 k~CP~C~~ 284 (478)
+-||+|+.
T Consensus 61 R~CP~C~~ 68 (111)
T PF14319_consen 61 RHCPSCQA 68 (111)
T ss_pred cCCCCCCC
Confidence 55666554
No 271
>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 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=29.68 E-value=30 Score=24.61 Aligned_cols=35 Identities=20% Similarity=0.523 Sum_probs=24.1
Q ss_pred ccccccccccccCC--ceecCCCCccchhhHHHHHHH
Q 011726 117 VMCDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIV 151 (478)
Q Consensus 117 ~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yi~~ 151 (478)
..|.+|-..|.... ..--.||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 46888877765321 122379999999999877543
No 273
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=29.66 E-value=32 Score=28.26 Aligned_cols=25 Identities=36% Similarity=1.060 Sum_probs=16.5
Q ss_pred cCCCCCCCC-ccccCCCCceEec-cccce
Q 011726 277 KPCPKCHKP-VEKNGGCNLVSCI-CGQAF 303 (478)
Q Consensus 277 k~CP~C~~~-IeK~~GCnhm~C~-C~~~F 303 (478)
.+||+|..- .-..+| +|.|. |.++|
T Consensus 4 p~cp~c~sEytYed~~--~~~cpec~~ew 30 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICPECAHEW 30 (112)
T ss_pred CCCCccCCceEEecCc--eEeCchhcccc
Confidence 589999754 445566 67774 66654
No 274
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.39 E-value=30 Score=31.57 Aligned_cols=24 Identities=33% Similarity=0.960 Sum_probs=16.4
Q ss_pred cCCCCCCCCccccCCCCceEe-ccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C-~C~~~ 302 (478)
-.|++|+.++++ .=+.|+| +||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 478888888887 3356777 47754
No 275
>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=29.25 E-value=27 Score=23.69 Aligned_cols=26 Identities=27% Similarity=0.677 Sum_probs=14.4
Q ss_pred CCCCceEEeccccceeeEec-CCccccccccCC
Q 011726 214 PHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSE 245 (478)
Q Consensus 214 p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~ 245 (478)
++|+.... ..+.|+ |+..||...+.+
T Consensus 4 ~~C~~~~~------~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 4 PGCKKKDF------LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp TTT--BCT------SHEE-TTTS-EE-TTTHST
T ss_pred CcCcCccC------CCeECCCCCcccCccccCc
Confidence 56754432 347998 999999997653
No 276
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.92 E-value=32 Score=24.86 Aligned_cols=13 Identities=23% Similarity=0.457 Sum_probs=10.2
Q ss_pred CCcCCCCCCCCcc
Q 011726 275 HTKPCPKCHKPVE 287 (478)
Q Consensus 275 ~~k~CP~C~~~Ie 287 (478)
+.-.||+|+.+..
T Consensus 25 ~l~~C~~cG~~~~ 37 (55)
T TIGR01031 25 TLVVCPNCGEFKL 37 (55)
T ss_pred cceECCCCCCccc
Confidence 3467999998877
No 277
>PHA02325 hypothetical protein
Probab=28.65 E-value=26 Score=25.88 Aligned_cols=11 Identities=55% Similarity=1.047 Sum_probs=6.6
Q ss_pred CCcCCCCCCCC
Q 011726 275 HTKPCPKCHKP 285 (478)
Q Consensus 275 ~~k~CP~C~~~ 285 (478)
++|.||+|++.
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 35677776653
No 278
>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=27.98 E-value=36 Score=33.21 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=21.9
Q ss_pred cCCCCCCCCceEEeccccceeeEecCCcccccccc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCL 243 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~ 243 (478)
-|| .|..-....++-...+. +|++..|-+|.
T Consensus 2 ~Cp---~CKt~~Y~np~lk~~in-~C~H~lCEsCv 32 (300)
T KOG3800|consen 2 ACP---KCKTDRYLNPDLKLMIN-ECGHRLCESCV 32 (300)
T ss_pred CCc---ccccceecCccceeeec-cccchHHHHHH
Confidence 477 68777666654444444 79999999985
No 279
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=27.94 E-value=38 Score=32.14 Aligned_cols=16 Identities=38% Similarity=0.885 Sum_probs=13.7
Q ss_pred cCCccccccccCCCCC
Q 011726 233 ACGAQFCFSCLSEAHS 248 (478)
Q Consensus 233 ~C~~~fC~~C~~~~H~ 248 (478)
.|++.||..|....|.
T Consensus 22 aC~HvfC~~C~k~~~~ 37 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSP 37 (233)
T ss_pred echhhhhhhhcccCCc
Confidence 4999999999987665
No 280
>PLN00209 ribosomal protein S27; Provisional
Probab=27.71 E-value=57 Score=25.79 Aligned_cols=34 Identities=24% Similarity=0.365 Sum_probs=25.5
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCccccccccC
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLS 244 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~ 244 (478)
..|| +|++.-.+-+.....|.|. ||...|.-=+.
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 4798 8998877666666679996 99998765443
No 281
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=27.71 E-value=54 Score=29.16 Aligned_cols=49 Identities=22% Similarity=0.442 Sum_probs=32.8
Q ss_pred ccccccccccccccCCceecCCCC---ccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVAGDKATKMDCGH---CFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH---~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
....|-||+++-. .......|.. ....+|+..|+..+ ....|+. |....
T Consensus 7 ~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPY 58 (162)
T ss_pred CCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeE
Confidence 4568999998853 2222224444 56899999999852 2478988 77654
No 282
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=27.53 E-value=57 Score=25.73 Aligned_cols=35 Identities=26% Similarity=0.511 Sum_probs=26.1
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCccccccccCC
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSE 245 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~ 245 (478)
..|| +|++.-.+-+.....|.|. ||...|.-=+..
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 4798 8998877666666679997 999988654443
No 283
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.01 E-value=42 Score=38.89 Aligned_cols=56 Identities=20% Similarity=0.517 Sum_probs=39.4
Q ss_pred CCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCC
Q 011726 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (478)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 293 (478)
-||--|....+....|-|. |+.-.|..|-.- . .+...+-||.|+....+--||.
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 5887777766666789997 999999988631 0 0123478999988887655655
Q ss_pred ce
Q 011726 294 LV 295 (478)
Q Consensus 294 hm 295 (478)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 43
No 284
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=26.93 E-value=24 Score=25.50 Aligned_cols=13 Identities=31% Similarity=0.818 Sum_probs=10.0
Q ss_pred CCcCCCCCCCCcc
Q 011726 275 HTKPCPKCHKPVE 287 (478)
Q Consensus 275 ~~k~CP~C~~~Ie 287 (478)
+...||.|+.+..
T Consensus 25 ~l~~c~~cg~~~~ 37 (56)
T PF01783_consen 25 NLVKCPNCGEPKL 37 (56)
T ss_dssp SEEESSSSSSEES
T ss_pred ceeeeccCCCEec
Confidence 4568999988776
No 285
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=26.91 E-value=2.1e+02 Score=21.00 Aligned_cols=41 Identities=15% Similarity=0.283 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHcCC-CHHHHHHHHHHcCCChHHHHHHHHhc
Q 011726 50 AQKEDLRRVMELLSL-REHHARTLLIHYRWDVEKLLAVLVEN 90 (478)
Q Consensus 50 ~~~~~i~~v~~~l~i-~~~~a~~lL~~~~W~~e~l~e~~~~~ 90 (478)
..++.|+.+.++.|- +..+..+.|+.++-+.+...+++...
T Consensus 4 ~~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 4 ASRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 456788999999999 88999999999999988877777643
No 286
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=26.64 E-value=1.6e+02 Score=24.74 Aligned_cols=36 Identities=28% Similarity=0.302 Sum_probs=30.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHHHHH
Q 011726 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVL 87 (478)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~e~~ 87 (478)
.++|.-|++..|++...|+..|...+||.-..+-.+
T Consensus 77 ~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L 112 (115)
T PRK06369 77 EEDIELVAEQTGVSEEEARKALEEANGDLAEAILKL 112 (115)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHH
Confidence 568889999999999999999999999976654433
No 287
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=26.35 E-value=1.7e+02 Score=24.67 Aligned_cols=33 Identities=21% Similarity=0.316 Sum_probs=29.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCChHHHH
Q 011726 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLL 84 (478)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~lL~~~~W~~e~l~ 84 (478)
.++|.-|++..|++...|+..|...+||.-..+
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI 111 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEECGGDLAEAI 111 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHH
Confidence 578899999999999999999999999976544
No 288
>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=26.26 E-value=51 Score=28.25 Aligned_cols=21 Identities=48% Similarity=1.262 Sum_probs=10.8
Q ss_pred cCCCC--CCCCccccCCCCceEec--cccce
Q 011726 277 KPCPK--CHKPVEKNGGCNLVSCI--CGQAF 303 (478)
Q Consensus 277 k~CP~--C~~~IeK~~GCnhm~C~--C~~~F 303 (478)
|+||+ |.-.++ +|-|+ |||-.
T Consensus 83 k~Cpn~~C~g~L~------~~pCrGh~GYPV 107 (143)
T PF03615_consen 83 KPCPNRNCKGRLE------LIPCRGHCGYPV 107 (143)
T ss_dssp SB-SS--S--BEE------EE---TBTTB--
T ss_pred CCCCccccCCcee------EEeccCcCCCce
Confidence 89999 998888 57884 77643
No 289
>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=26.16 E-value=22 Score=39.81 Aligned_cols=48 Identities=33% Similarity=0.803 Sum_probs=0.0
Q ss_pred HhhCCCcccCCCCCCCCceEEeccccceeeEec-CCcc-----ccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHh
Q 011726 201 IEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ-----FCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITV 274 (478)
Q Consensus 201 v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~-----fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~ 274 (478)
+...-..+.|| .|+..... ..|+ ||.. +|..|+...-.
T Consensus 649 i~vei~~r~Cp---~Cg~~t~~-------~~Cp~CG~~T~~~~~Cp~C~~~~~~-------------------------- 692 (900)
T PF03833_consen 649 IEVEIGRRRCP---KCGKETFY-------NRCPECGSHTEPVYVCPDCGIEVEE-------------------------- 692 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred eEEeeecccCc---ccCCcchh-------hcCcccCCccccceeccccccccCc--------------------------
Q ss_pred CCcCCCCCCCCc
Q 011726 275 HTKPCPKCHKPV 286 (478)
Q Consensus 275 ~~k~CP~C~~~I 286 (478)
..||+|+...
T Consensus 693 --~~C~~C~~~~ 702 (900)
T PF03833_consen 693 --DECPKCGRET 702 (900)
T ss_dssp ------------
T ss_pred --cccccccccC
No 290
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=26.10 E-value=31 Score=28.67 Aligned_cols=12 Identities=50% Similarity=1.265 Sum_probs=10.5
Q ss_pred ceEeccccceec
Q 011726 294 LVSCICGQAFCW 305 (478)
Q Consensus 294 hm~C~C~~~FCw 305 (478)
-+.|.|||.||-
T Consensus 24 ~vkc~CGh~f~d 35 (112)
T PF08882_consen 24 VVKCDCGHEFCD 35 (112)
T ss_pred eeeccCCCeecC
Confidence 588999999985
No 291
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.09 E-value=39 Score=24.57 Aligned_cols=29 Identities=34% Similarity=0.794 Sum_probs=20.2
Q ss_pred CCcCCCCCCCCccccCCCCceEeccccceeccccccccCCCC
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRDHT 316 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~H~ 316 (478)
..+.||+|++.-- ...|-.||++....|.
T Consensus 4 ~mr~C~~CgvYTL-------------k~~CP~CG~~t~~~~P 32 (56)
T PRK13130 4 KIRKCPKCGVYTL-------------KEICPVCGGKTKNPHP 32 (56)
T ss_pred cceECCCCCCEEc-------------cccCcCCCCCCCCCCC
Confidence 4578999987655 3557778888665553
No 292
>PRK00420 hypothetical protein; Validated
Probab=25.76 E-value=1.4e+02 Score=25.12 Aligned_cols=43 Identities=23% Similarity=0.329 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHHHHHhhCCCcccCCCCCCCCceEEeccccceeeEecCCccccccccC
Q 011726 187 NLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLS 244 (478)
Q Consensus 187 e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~ 244 (478)
+..++..+.+++-+..- -..|| .|+..+..... |..||..|+.
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 33444445555433221 25898 69987664211 4556667765
No 293
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=25.64 E-value=35 Score=25.06 Aligned_cols=23 Identities=39% Similarity=0.986 Sum_probs=16.2
Q ss_pred cCCCCCCCCccccCCCCceEeccccceec-ccccc
Q 011726 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCW-LCGGA 310 (478)
Q Consensus 277 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw-~C~~~ 310 (478)
|-||.||.+|.- ...||- .|...
T Consensus 4 kHC~~CG~~Ip~-----------~~~fCS~~C~~~ 27 (59)
T PF09889_consen 4 KHCPVCGKPIPP-----------DESFCSPKCREE 27 (59)
T ss_pred CcCCcCCCcCCc-----------chhhhCHHHHHH
Confidence 689999999883 245663 66655
No 294
>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=25.42 E-value=31 Score=27.10 Aligned_cols=28 Identities=36% Similarity=1.056 Sum_probs=11.6
Q ss_pred CcCCCCCCCC------ccccCCCCceEe-ccccce
Q 011726 276 TKPCPKCHKP------VEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 276 ~k~CP~C~~~------IeK~~GCnhm~C-~C~~~F 303 (478)
.=.||.|+.. |.+..|=-++.| .||..|
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 334455556777 365544
No 295
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.34 E-value=25 Score=31.15 Aligned_cols=28 Identities=18% Similarity=0.532 Sum_probs=20.4
Q ss_pred cccccccccccccccC-CceecCCCCccc
Q 011726 114 SSTVMCDICMEEVAGD-KATKMDCGHCFC 141 (478)
Q Consensus 114 ~~~~~C~IC~e~~~~~-~~~~l~CgH~fC 141 (478)
....+|.||++++... .+..|+|-..|.
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEee
Confidence 4568999999997654 455688876554
No 296
>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=25.07 E-value=29 Score=22.57 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=14.7
Q ss_pred cchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 140 FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 140 fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
.|.+|++.|....-+-=....+.|+. |+-.
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 48889988865432111235788887 7643
No 297
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=24.80 E-value=24 Score=38.71 Aligned_cols=49 Identities=27% Similarity=0.618 Sum_probs=35.6
Q ss_pred ccccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCcc
Q 011726 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (478)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~~ 172 (478)
...+|+||+..+ ..+..+.|.|.||..||..-+...-. ...||. |...+
T Consensus 20 k~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~ 68 (684)
T KOG4362|consen 20 KILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDI 68 (684)
T ss_pred hhccCCceeEEe--eccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhh
Confidence 357899999986 34577899999999999887765321 456776 65433
No 298
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.70 E-value=52 Score=31.88 Aligned_cols=28 Identities=18% Similarity=0.444 Sum_probs=20.6
Q ss_pred CCcCCCCCCCCccccCCCCceEe-ccccc
Q 011726 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 275 ~~k~CP~C~~~IeK~~GCnhm~C-~C~~~ 302 (478)
+.+-||.|+.++....|=..+.| .||..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 46899999998876544466888 58743
No 299
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=24.64 E-value=42 Score=39.08 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=7.8
Q ss_pred CCCCCCCccccCCCCce
Q 011726 279 CPKCHKPVEKNGGCNLV 295 (478)
Q Consensus 279 CP~C~~~IeK~~GCnhm 295 (478)
=|+|-.-+--.+.|--|
T Consensus 2281 r~kclfE~rn~g~~Lam 2297 (3015)
T KOG0943|consen 2281 RGKCLFEVRNDGNCLAM 2297 (3015)
T ss_pred CCcceEEEecCCceeec
Confidence 34555444444444433
No 300
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=24.28 E-value=33 Score=33.75 Aligned_cols=28 Identities=25% Similarity=0.776 Sum_probs=19.2
Q ss_pred CcCCCCCCCCccccCCCCceEec---cccceecccccc
Q 011726 276 TKPCPKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGA 310 (478)
Q Consensus 276 ~k~CP~C~~~IeK~~GCnhm~C~---C~~~FCw~C~~~ 310 (478)
..-|-+|..+|- ++=| |++.||+.|...
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 367999999997 4442 666666666544
No 301
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=24.05 E-value=40 Score=29.72 Aligned_cols=35 Identities=11% Similarity=0.021 Sum_probs=25.4
Q ss_pred eCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHc
Q 011726 42 ITRESLLAAQKEDLRRVMELLSLREHHARTLLIHY 76 (478)
Q Consensus 42 l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~lL~~~ 76 (478)
.+.++|...+.+....+.+.-.++.+.+..+-.+.
T Consensus 11 ~~~~~L~~~le~a~e~~~~~~elT~eEl~lv~~yl 45 (146)
T PF07295_consen 11 HSEEELQEALEKAKEYLVAAGELTREELALVSAYL 45 (146)
T ss_pred cCHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Confidence 36778888888888888888888887766555433
No 302
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.04 E-value=49 Score=28.46 Aligned_cols=23 Identities=43% Similarity=1.014 Sum_probs=14.5
Q ss_pred ccCCCCCCCCceEEeccccceeeEec-CCc
Q 011726 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGA 236 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~ 236 (478)
..|| .||..+...++ .|.|| |++
T Consensus 29 ~hCp---~Cg~PLF~KdG---~v~CPvC~~ 52 (131)
T COG1645 29 KHCP---KCGTPLFRKDG---EVFCPVCGY 52 (131)
T ss_pred hhCc---ccCCcceeeCC---eEECCCCCc
Confidence 4898 79988776432 25555 554
No 303
>PLN02436 cellulose synthase A
Probab=24.00 E-value=55 Score=37.91 Aligned_cols=56 Identities=25% Similarity=0.570 Sum_probs=39.0
Q ss_pred CCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCC
Q 011726 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (478)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 293 (478)
-||--|....+....|-|. |+...|..|-.- . . +...+.||.|+....+--|++
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------R---------REGNQACPQCKTRYKRIKGSP 95 (1094)
T ss_pred ccccccCcCCCCCEEEeeccCCCccccchhhh----------h------h---------hcCCccCcccCCchhhccCCC
Confidence 5777776666666779998 999999998631 0 0 123378999998888665665
Q ss_pred ce
Q 011726 294 LV 295 (478)
Q Consensus 294 hm 295 (478)
.+
T Consensus 96 ~~ 97 (1094)
T PLN02436 96 RV 97 (1094)
T ss_pred Cc
Confidence 43
No 304
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=23.48 E-value=37 Score=32.55 Aligned_cols=47 Identities=19% Similarity=0.364 Sum_probs=35.2
Q ss_pred ccccccccccccCCceecCCCCccchhhHHHHHHHHHhcCCcccccCCCcccCC
Q 011726 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (478)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~ 170 (478)
..|||=+-.+- ..+++-.|||.|=++=+..++... ..++||..+|..
T Consensus 177 ~rdPis~~~I~-nPviSkkC~HvydrDsI~~~l~~~------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 177 NRDPISKKPIV-NPVISKKCGHVYDRDSIMQILCDE------ITIRCPVLGCEN 223 (262)
T ss_pred ccCchhhhhhh-chhhhcCcCcchhhhhHHHHhccC------ceeecccccCCc
Confidence 56888665542 345567999999999888887641 468999999994
No 305
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.27 E-value=72 Score=26.75 Aligned_cols=29 Identities=28% Similarity=0.783 Sum_probs=18.9
Q ss_pred cccCCCCCCCCceEEecc-ccceeeEec-CCccc
Q 011726 207 VKWCPSTPHCGNAIRVEE-VEVCEVECA-CGAQF 238 (478)
Q Consensus 207 ~~~CP~~p~C~~~i~~~~-~~~~~v~C~-C~~~f 238 (478)
+++|| .|++.+.+.. .......|+ ||+.+
T Consensus 2 m~FCp---~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP---KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC---CccCeeEEeEcCCCcEEECCCCCcch
Confidence 56898 7999988643 122246775 77664
No 306
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.09 E-value=42 Score=36.30 Aligned_cols=29 Identities=41% Similarity=0.826 Sum_probs=21.8
Q ss_pred CCcCCCC--CCCCccccCCCCceEe-ccccce
Q 011726 275 HTKPCPK--CHKPVEKNGGCNLVSC-ICGQAF 303 (478)
Q Consensus 275 ~~k~CP~--C~~~IeK~~GCnhm~C-~C~~~F 303 (478)
+...||+ |+..+.+...=+|..| .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 4467884 8888888888888888 477665
No 307
>COG4640 Predicted membrane protein [Function unknown]
Probab=23.00 E-value=43 Score=34.12 Aligned_cols=8 Identities=63% Similarity=1.327 Sum_probs=5.9
Q ss_pred cCCCCCCC
Q 011726 277 KPCPKCHK 284 (478)
Q Consensus 277 k~CP~C~~ 284 (478)
+.||+||.
T Consensus 2 ~fC~kcG~ 9 (465)
T COG4640 2 KFCPKCGS 9 (465)
T ss_pred Cccccccc
Confidence 57888884
No 308
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.58 E-value=49 Score=32.85 Aligned_cols=35 Identities=23% Similarity=0.545 Sum_probs=22.6
Q ss_pred cccccccccccCCceec-CCCCccchhhHHHHHHHHH
Q 011726 118 MCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKI 153 (478)
Q Consensus 118 ~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~i 153 (478)
.|-.|.++......+.. .|.+.||.+|= .|+...+
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCD-v~iHesL 367 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCD-VFIHESL 367 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccch-HHHHhhh
Confidence 38888766544444554 78899999983 3444433
No 309
>PLN02436 cellulose synthase A
Probab=22.31 E-value=71 Score=37.07 Aligned_cols=48 Identities=27% Similarity=0.611 Sum_probs=33.2
Q ss_pred cccccccccccccc---CCce-ec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 115 STVMCDICMEEVAG---DKAT-KM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 115 ~~~~C~IC~e~~~~---~~~~-~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
....|.||.+++.. .+++ .. .|+-..|+.|. +|-. ++|. -.||+ |+..
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg~---~~Cpq--ckt~ 87 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REGN---QACPQ--CKTR 87 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC---ccCcc--cCCc
Confidence 34689999999643 2333 34 68889999999 5543 4565 57988 7654
No 310
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.26 E-value=36 Score=33.54 Aligned_cols=34 Identities=32% Similarity=0.970 Sum_probs=16.4
Q ss_pred cCCCCCCCC-----ccccC--CCCceEe-ccccce------ecccccc
Q 011726 277 KPCPKCHKP-----VEKNG--GCNLVSC-ICGQAF------CWLCGGA 310 (478)
Q Consensus 277 k~CP~C~~~-----IeK~~--GCnhm~C-~C~~~F------Cw~C~~~ 310 (478)
..||-||.+ |...+ |=-+++| .|+++| |-.|+..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 689999975 23333 7899999 599887 9999876
No 311
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.17 E-value=1.6e+02 Score=20.08 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=15.0
Q ss_pred CcCCCCCCCC-ccccCCCCceEec-ccc
Q 011726 276 TKPCPKCHKP-VEKNGGCNLVSCI-CGQ 301 (478)
Q Consensus 276 ~k~CP~C~~~-IeK~~GCnhm~C~-C~~ 301 (478)
.-.||+|+.. +-+..+=....|+ |++
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 3569999974 2233333446663 664
No 312
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=22.10 E-value=2.4e+02 Score=29.68 Aligned_cols=41 Identities=17% Similarity=0.205 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHcC-------CCHHHHHHHHHHcCCChHHHHHHH
Q 011726 47 LLAAQKEDLRRVMELLS-------LREHHARTLLIHYRWDVEKLLAVL 87 (478)
Q Consensus 47 i~~~~~~~i~~v~~~l~-------i~~~~a~~lL~~~~W~~e~l~e~~ 87 (478)
+...-.+.|.+|+.--+ -|..+-.+|..||+=.+..|-+.-
T Consensus 258 leekhr~rmd~VmkEW~~ae~qaKnPKAekqalnqhFQ~~v~sLEee~ 305 (615)
T KOG3540|consen 258 LEEKHRKRMDKVMKEWEEAETQAKNPKAEKQALNQHFQKTVSSLEEEA 305 (615)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccCchhhHHHHHHHHHHHHHHHHHHH
Confidence 33334455666663221 144555788888877766665543
No 313
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=21.95 E-value=53 Score=25.57 Aligned_cols=17 Identities=24% Similarity=0.577 Sum_probs=16.2
Q ss_pred CCCCccchhhHHHHHHH
Q 011726 135 DCGHCFCNDCWTEHFIV 151 (478)
Q Consensus 135 ~CgH~fC~~C~~~yi~~ 151 (478)
-|.|.|..-|+.+++.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 69999999999999987
No 314
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.84 E-value=50 Score=26.30 Aligned_cols=17 Identities=18% Similarity=0.626 Sum_probs=14.2
Q ss_pred ccchhhHHHHHHHHHhc
Q 011726 139 CFCNDCWTEHFIVKINE 155 (478)
Q Consensus 139 ~fC~~C~~~yi~~~i~~ 155 (478)
-||++|+..|+..+-..
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887643
No 315
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.72 E-value=50 Score=21.59 Aligned_cols=13 Identities=31% Similarity=0.815 Sum_probs=10.3
Q ss_pred cCCCCCCCCcccc
Q 011726 277 KPCPKCHKPVEKN 289 (478)
Q Consensus 277 k~CP~C~~~IeK~ 289 (478)
..||.|+..++|.
T Consensus 27 ~~CP~Cg~~~~r~ 39 (41)
T smart00834 27 ATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCcceec
Confidence 6899999877653
No 316
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.21 E-value=38 Score=31.71 Aligned_cols=80 Identities=21% Similarity=0.537 Sum_probs=47.8
Q ss_pred ccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCCceEeccccceeccccccccCCC
Q 011726 236 AQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRDH 315 (478)
Q Consensus 236 ~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~H 315 (478)
...|..|....|..+--..+-.|+.... -.-.|.-|+++++. |.|-.+ .|-+-|=|.|+..|...-
T Consensus 21 VNVCEhClV~nHpkCiVQSYLqWL~DsD-----------Y~pNC~LC~t~La~-gdt~RL--vCyhlfHW~ClneraA~l 86 (299)
T KOG3970|consen 21 VNVCEHCLVANHPKCIVQSYLQWLQDSD-----------YNPNCRLCNTPLAS-GDTTRL--VCYHLFHWKCLNERAANL 86 (299)
T ss_pred hhHHHHHHhccCchhhHHHHHHHHhhcC-----------CCCCCceeCCcccc-Ccceee--hhhhhHHHHHhhHHHhhC
Confidence 3456677777887665555555553211 12478888988873 222211 388899999998875433
Q ss_pred Cccc-cCCCcCCCCc
Q 011726 316 TWSR-IAGHSCGRYK 329 (478)
Q Consensus 316 ~~~~-~~~~~C~~~~ 329 (478)
.-++ ..||.|+.-.
T Consensus 87 PanTAPaGyqCP~Cs 101 (299)
T KOG3970|consen 87 PANTAPAGYQCPCCS 101 (299)
T ss_pred CCcCCCCcccCCCCC
Confidence 2222 3578877543
No 317
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.13 E-value=66 Score=37.22 Aligned_cols=55 Identities=27% Similarity=0.663 Sum_probs=37.7
Q ss_pred CCCceEEeccccceeeEec-CCccccccccCCCCCCCCcchhHHHHHHhhhhHHHHHHHHhCCcCCCCCCCCccccCCCC
Q 011726 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (478)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 293 (478)
-||--|....+....|-|. |+...|..|-.- - .+...+.||.|+....+--|++
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 5777666666666779997 999999988631 0 0123378888888887655554
Q ss_pred c
Q 011726 294 L 294 (478)
Q Consensus 294 h 294 (478)
.
T Consensus 75 ~ 75 (1044)
T PLN02915 75 R 75 (1044)
T ss_pred C
Confidence 4
No 318
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=21.09 E-value=70 Score=24.43 Aligned_cols=26 Identities=35% Similarity=0.816 Sum_probs=18.6
Q ss_pred cCCCCCCCCc----cccCCCCceEe-ccccc
Q 011726 277 KPCPKCHKPV----EKNGGCNLVSC-ICGQA 302 (478)
Q Consensus 277 k~CP~C~~~I----eK~~GCnhm~C-~C~~~ 302 (478)
-.||+|+.+= -+..|=.++.| .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 4799998642 24566778889 59875
No 319
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.85 E-value=61 Score=21.16 Aligned_cols=30 Identities=30% Similarity=0.864 Sum_probs=17.5
Q ss_pred HHHhCCcCCCCCCCCcc-ccCCCCceEe-ccccc
Q 011726 271 WITVHTKPCPKCHKPVE-KNGGCNLVSC-ICGQA 302 (478)
Q Consensus 271 ~i~~~~k~CP~C~~~Ie-K~~GCnhm~C-~C~~~ 302 (478)
|+....-+||.|+...- .++| ..+| +||+.
T Consensus 3 ~~~~~~~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred ccccCCCcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 33333457999987643 2444 3667 57664
No 320
>PLN02189 cellulose synthase
Probab=20.85 E-value=70 Score=37.03 Aligned_cols=48 Identities=27% Similarity=0.674 Sum_probs=33.2
Q ss_pred cccccccccccccc---CCc-eec-CCCCccchhhHHHHHHHHHhcCCcccccCCCcccCCc
Q 011726 115 STVMCDICMEEVAG---DKA-TKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (478)
Q Consensus 115 ~~~~C~IC~e~~~~---~~~-~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~i~CP~~~C~~~ 171 (478)
....|.||.+++.. .++ +.. .|+-..|+.|. +|-. ++|. -.||+ |+..
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg~---q~Cpq--Ckt~ 85 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REGT---QNCPQ--CKTR 85 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC---ccCcc--cCCc
Confidence 34689999999653 233 334 58889999999 5533 4665 47988 7754
No 321
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=20.84 E-value=51 Score=20.62 Aligned_cols=11 Identities=45% Similarity=0.848 Sum_probs=6.9
Q ss_pred cCCCCCCCCcc
Q 011726 277 KPCPKCHKPVE 287 (478)
Q Consensus 277 k~CP~C~~~Ie 287 (478)
..||+|+.-+-
T Consensus 2 hlcpkcgvgvl 12 (36)
T PF09151_consen 2 HLCPKCGVGVL 12 (36)
T ss_dssp -B-TTTSSSBE
T ss_pred ccCCccCceEE
Confidence 36999998653
No 322
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=20.77 E-value=87 Score=30.08 Aligned_cols=16 Identities=31% Similarity=0.764 Sum_probs=13.1
Q ss_pred ccCCCCCCCCceEEecc
Q 011726 208 KWCPSTPHCGNAIRVEE 224 (478)
Q Consensus 208 ~~CP~~p~C~~~i~~~~ 224 (478)
.-|| +|+|.++|...+
T Consensus 124 IaCP-Rp~CkRiI~L~~ 139 (256)
T PF09788_consen 124 IACP-RPNCKRIINLGP 139 (256)
T ss_pred ccCC-CCCCcceEEeCC
Confidence 4799 699999998654
No 323
>PF15616 TerY-C: TerY-C metal binding domain
Probab=20.75 E-value=67 Score=27.73 Aligned_cols=35 Identities=31% Similarity=0.763 Sum_probs=19.1
Q ss_pred CCcCCCCCCCCcc-ccCCCCceEec--cccceeccccc
Q 011726 275 HTKPCPKCHKPVE-KNGGCNLVSCI--CGQAFCWLCGG 309 (478)
Q Consensus 275 ~~k~CP~C~~~Ie-K~~GCnhm~C~--C~~~FCw~C~~ 309 (478)
..--||.|+...- -.-+|++++|. =+..-|.-|+.
T Consensus 76 g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~ 113 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGN 113 (131)
T ss_pred CCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCC
Confidence 3468999998743 22345555551 33444444544
No 324
>PF15616 TerY-C: TerY-C metal binding domain
Probab=20.49 E-value=60 Score=27.99 Aligned_cols=23 Identities=48% Similarity=1.214 Sum_probs=17.4
Q ss_pred cCCCCCCCCceEEeccccceeeEecCCcccccc
Q 011726 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFS 241 (478)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~ 241 (478)
-|| .|++... .+.|.||..+|..
T Consensus 79 gCP---~CGn~~~-------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 79 GCP---HCGNQYA-------FAVCGCGKLFCID 101 (131)
T ss_pred CCC---CCcChhc-------EEEecCCCEEEeC
Confidence 566 7887643 3788999999986
No 325
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=20.23 E-value=54 Score=20.54 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=12.3
Q ss_pred cccCCCcccCCccCHHHHHHHhc
Q 011726 160 RIRCMAHKCNAICDEAVVRNLVS 182 (478)
Q Consensus 160 ~i~CP~~~C~~~~~~~~i~~ll~ 182 (478)
.++||..+|...+...-....++
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~H~s 24 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSHHLS 24 (30)
T ss_dssp EEE--STT---EEEHHHHHHHHH
T ss_pred ccccccccCcchhhhhhhccccc
Confidence 47999999998877665555554
Done!