Query 007785
Match_columns 590
No_of_seqs 416 out of 1551
Neff 6.9
Searched_HMMs 46136
Date Thu Mar 28 15:18:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007785hhsearch_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 1.2E-67 2.5E-72 575.3 26.1 429 41-497 2-437 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 4.3E-34 9.2E-39 304.5 10.2 223 115-363 145-374 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 1.2E-33 2.6E-38 290.2 11.9 205 114-323 182-416 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.7E-24 3.7E-29 215.2 8.2 197 113-318 218-442 (446)
5 smart00647 IBR In Between Ring 99.2 3.2E-11 6.9E-16 96.2 5.8 62 190-252 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 3.6E-11 7.8E-16 95.8 2.1 62 190-252 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.5 4.2E-08 9E-13 71.9 2.0 41 119-165 1-41 (42)
8 PF13923 zf-C3HC4_2: Zinc fing 98.1 1.3E-06 2.8E-11 62.9 2.3 37 119-165 1-38 (39)
9 PF13639 zf-RING_2: Ring finge 98.1 1.4E-06 3.1E-11 64.3 2.1 40 118-165 2-42 (44)
10 PF00097 zf-C3HC4: Zinc finger 98.1 2.1E-06 4.6E-11 62.3 2.8 39 119-165 1-40 (41)
11 smart00647 IBR In Between Ring 98.0 8.4E-06 1.8E-10 64.8 4.7 38 275-312 17-59 (64)
12 KOG0320 Predicted E3 ubiquitin 98.0 3.3E-06 7.1E-11 79.6 2.6 53 114-176 129-181 (187)
13 PLN03208 E3 ubiquitin-protein 98.0 4.9E-06 1.1E-10 80.3 3.6 64 114-181 16-87 (193)
14 PF13445 zf-RING_UBOX: RING-ty 97.9 5.1E-06 1.1E-10 61.1 2.3 41 119-164 1-43 (43)
15 PF01485 IBR: IBR domain; Int 97.9 4.7E-06 1E-10 66.1 2.1 39 275-313 17-60 (64)
16 PF13920 zf-C3HC4_3: Zinc fing 97.8 1.9E-05 4E-10 60.0 3.0 46 116-173 2-48 (50)
17 cd00162 RING RING-finger (Real 97.7 3.2E-05 6.8E-10 56.1 3.2 43 118-171 1-44 (45)
18 PF14634 zf-RING_5: zinc-RING 97.7 2.4E-05 5.1E-10 57.9 2.2 42 118-169 1-43 (44)
19 KOG2164 Predicted E3 ubiquitin 97.5 2.8E-05 6.1E-10 84.1 1.5 60 116-182 186-245 (513)
20 KOG0823 Predicted E3 ubiquitin 97.5 3.4E-05 7.3E-10 75.9 1.8 56 114-178 45-100 (230)
21 smart00504 Ubox Modified RING 97.5 9.2E-05 2E-09 58.6 3.3 47 117-175 2-48 (63)
22 smart00184 RING Ring finger. E 97.5 8.3E-05 1.8E-09 51.9 2.5 38 119-165 1-38 (39)
23 KOG2177 Predicted E3 ubiquitin 97.4 9.3E-05 2E-09 75.5 2.9 44 114-169 11-54 (386)
24 PHA02926 zinc finger-like prot 97.3 0.00013 2.7E-09 71.5 2.6 56 113-172 167-229 (242)
25 TIGR00599 rad18 DNA repair pro 97.3 0.00014 3.1E-09 78.1 3.1 66 114-194 24-90 (397)
26 KOG0317 Predicted E3 ubiquitin 97.3 0.00011 2.3E-09 74.5 1.7 51 115-177 238-288 (293)
27 PHA02929 N1R/p28-like protein; 97.2 0.00019 4E-09 72.2 3.1 50 114-173 172-227 (238)
28 KOG0287 Postreplication repair 97.1 0.0003 6.4E-09 72.3 3.0 64 115-193 22-86 (442)
29 KOG0804 Cytoplasmic Zn-finger 97.0 0.1 2.3E-06 56.1 20.4 120 40-171 84-220 (493)
30 KOG4367 Predicted Zn-finger pr 97.0 0.004 8.7E-08 66.0 9.8 35 115-151 3-37 (699)
31 KOG0978 E3 ubiquitin ligase in 96.5 0.00065 1.4E-08 77.1 -0.0 56 114-180 641-696 (698)
32 TIGR00570 cdk7 CDK-activating 96.5 0.0015 3.3E-08 67.7 2.4 53 117-178 4-59 (309)
33 PF11789 zf-Nse: Zinc-finger o 96.4 0.0023 5E-08 50.1 2.4 47 115-169 10-57 (57)
34 PF04564 U-box: U-box domain; 96.3 0.0023 4.9E-08 52.7 2.1 49 115-174 3-51 (73)
35 PF14835 zf-RING_6: zf-RING of 96.0 0.0013 2.8E-08 52.2 -0.7 43 116-172 7-50 (65)
36 PF14555 UBA_4: UBA-like domai 96.0 0.021 4.5E-07 42.0 5.5 40 52-91 1-40 (43)
37 COG5540 RING-finger-containing 95.9 0.005 1.1E-07 62.8 2.7 52 114-174 321-373 (374)
38 COG5574 PEX10 RING-finger-cont 95.8 0.0052 1.1E-07 61.8 2.2 53 115-177 214-266 (271)
39 KOG4628 Predicted E3 ubiquitin 95.7 0.0073 1.6E-07 63.7 3.1 45 117-168 230-275 (348)
40 KOG1002 Nucleotide excision re 95.7 0.0053 1.2E-07 66.6 1.9 56 113-175 533-588 (791)
41 PF12678 zf-rbx1: RING-H2 zinc 95.5 0.0079 1.7E-07 49.5 2.1 41 117-165 20-71 (73)
42 COG5432 RAD18 RING-finger-cont 95.0 0.013 2.8E-07 59.5 2.0 47 115-173 24-70 (391)
43 PF11793 FANCL_C: FANCL C-term 94.2 0.028 6.2E-07 45.9 2.0 56 116-173 2-66 (70)
44 KOG0824 Predicted E3 ubiquitin 94.1 0.026 5.5E-07 57.9 1.7 54 114-178 5-58 (324)
45 KOG2879 Predicted E3 ubiquitin 93.6 0.13 2.9E-06 52.1 5.9 51 113-173 236-287 (298)
46 KOG1814 Predicted E3 ubiquitin 93.4 0.25 5.3E-06 52.9 7.6 39 274-312 271-312 (445)
47 COG5243 HRD1 HRD ubiquitin lig 93.2 0.056 1.2E-06 56.7 2.6 48 115-172 286-344 (491)
48 PF14570 zf-RING_4: RING/Ubox 92.9 0.064 1.4E-06 40.4 1.8 44 119-171 1-46 (48)
49 KOG1812 Predicted E3 ubiquitin 92.8 0.046 1E-06 59.2 1.3 41 205-249 304-344 (384)
50 KOG4159 Predicted E3 ubiquitin 92.6 0.14 2.9E-06 55.6 4.5 49 114-174 82-130 (398)
51 KOG0311 Predicted E3 ubiquitin 92.4 0.027 5.8E-07 58.9 -1.1 47 115-171 42-88 (381)
52 PF10571 UPF0547: Uncharacteri 92.1 0.067 1.5E-06 35.0 0.9 23 277-303 1-24 (26)
53 TIGR00570 cdk7 CDK-activating 92.0 5.7 0.00012 41.7 15.4 53 209-290 5-57 (309)
54 COG5152 Uncharacterized conser 91.9 0.05 1.1E-06 52.4 0.3 32 115-148 195-226 (259)
55 KOG1039 Predicted E3 ubiquitin 91.7 0.11 2.5E-06 55.0 2.6 56 113-171 158-219 (344)
56 KOG0006 E3 ubiquitin-protein l 91.5 0.5 1.1E-05 48.8 6.7 148 72-250 286-439 (446)
57 KOG2660 Locus-specific chromos 91.3 0.11 2.5E-06 53.9 2.1 46 115-172 14-60 (331)
58 KOG0826 Predicted E3 ubiquitin 90.9 0.5 1.1E-05 49.2 6.2 48 115-172 299-347 (357)
59 KOG4185 Predicted E3 ubiquitin 90.8 0.29 6.2E-06 51.0 4.6 55 117-180 4-64 (296)
60 KOG1428 Inhibitor of type V ad 90.4 0.38 8.3E-06 58.1 5.4 66 115-182 3485-3553(3738)
61 KOG2817 Predicted E3 ubiquitin 90.3 1.2 2.6E-05 47.7 8.5 126 40-177 255-389 (394)
62 KOG0802 E3 ubiquitin ligase [P 90.0 0.15 3.3E-06 57.9 1.8 45 116-168 291-338 (543)
63 PRK00420 hypothetical protein; 89.6 2.9 6.2E-05 37.4 9.1 27 276-310 23-49 (112)
64 KOG1645 RING-finger-containing 89.2 0.25 5.5E-06 52.7 2.5 49 116-172 4-55 (463)
65 KOG4692 Predicted E3 ubiquitin 88.4 0.27 5.9E-06 51.4 2.1 52 111-174 417-468 (489)
66 PF12861 zf-Apc11: Anaphase-pr 87.8 0.42 9.1E-06 40.4 2.5 31 135-172 51-81 (85)
67 KOG1785 Tyrosine kinase negati 86.6 0.29 6.4E-06 51.9 1.2 47 116-170 369-415 (563)
68 smart00744 RINGv The RING-vari 86.2 0.54 1.2E-05 35.6 2.1 42 118-165 1-47 (49)
69 COG5220 TFB3 Cdk activating ki 86.2 0.19 4.1E-06 50.0 -0.5 49 117-172 11-63 (314)
70 KOG4265 Predicted E3 ubiquitin 86.1 0.65 1.4E-05 49.0 3.4 48 114-173 288-336 (349)
71 KOG1734 Predicted RING-contain 85.9 0.41 8.8E-06 48.5 1.7 52 115-174 223-282 (328)
72 KOG0828 Predicted E3 ubiquitin 85.4 0.45 9.7E-06 51.9 1.8 52 113-173 568-634 (636)
73 PF05883 Baculo_RING: Baculovi 84.7 0.39 8.4E-06 44.0 0.8 34 116-149 26-66 (134)
74 KOG4445 Uncharacterized conser 83.7 2.8 6E-05 43.3 6.5 37 117-153 116-153 (368)
75 PF13240 zinc_ribbon_2: zinc-r 83.6 0.53 1.2E-05 29.9 0.9 12 278-289 1-12 (23)
76 KOG1701 Focal adhesion adaptor 82.7 0.71 1.5E-05 49.7 1.9 69 225-300 378-459 (468)
77 KOG0825 PHD Zn-finger protein 82.5 0.83 1.8E-05 52.4 2.4 18 136-153 121-138 (1134)
78 PF00627 UBA: UBA/TS-N domain; 82.1 4.6 0.0001 28.3 5.3 34 52-86 3-36 (37)
79 KOG1001 Helicase-like transcri 81.6 0.55 1.2E-05 54.5 0.7 47 117-174 455-501 (674)
80 smart00661 RPOL9 RNA polymeras 81.2 1.3 2.9E-05 33.4 2.5 27 277-303 1-30 (52)
81 KOG4739 Uncharacterized protei 81.1 0.4 8.8E-06 48.0 -0.5 45 117-173 4-48 (233)
82 COG4647 AcxC Acetone carboxyla 80.2 4 8.7E-05 37.0 5.4 110 172-287 17-131 (165)
83 KOG0823 Predicted E3 ubiquitin 79.6 1.1 2.3E-05 44.7 1.9 42 222-287 54-95 (230)
84 KOG1815 Predicted E3 ubiquitin 79.5 1.1 2.3E-05 49.7 2.1 37 276-312 158-197 (444)
85 KOG1813 Predicted E3 ubiquitin 78.9 0.76 1.6E-05 47.3 0.6 45 116-172 241-285 (313)
86 PHA00626 hypothetical protein 78.6 1.6 3.4E-05 33.8 2.0 29 278-306 2-36 (59)
87 PRK14559 putative protein seri 78.1 1.3 2.9E-05 51.1 2.3 25 277-312 28-52 (645)
88 PF02845 CUE: CUE domain; Int 77.8 8 0.00017 28.0 5.6 38 52-89 2-40 (42)
89 KOG0297 TNF receptor-associate 77.1 1.5 3.2E-05 47.8 2.2 47 113-171 18-65 (391)
90 PF13248 zf-ribbon_3: zinc-rib 76.6 1.3 2.8E-05 28.9 0.9 12 277-288 3-14 (26)
91 KOG4172 Predicted E3 ubiquitin 76.6 0.76 1.6E-05 35.4 -0.2 45 117-172 8-53 (62)
92 PF14952 zf-tcix: Putative tre 75.1 1.9 4E-05 31.7 1.5 30 270-303 5-37 (44)
93 KOG0827 Predicted E3 ubiquitin 75.0 1.1 2.3E-05 47.8 0.4 48 116-170 4-53 (465)
94 PF04641 Rtf2: Rtf2 RING-finge 74.1 2.3 5.1E-05 43.6 2.6 58 114-182 111-170 (260)
95 KOG0317 Predicted E3 ubiquitin 73.6 0.52 1.1E-05 48.3 -2.2 35 272-312 235-270 (293)
96 PRK00432 30S ribosomal protein 72.8 2 4.3E-05 32.7 1.3 29 274-304 18-48 (50)
97 KOG3800 Predicted E3 ubiquitin 72.5 3.8 8.3E-05 42.2 3.6 48 118-174 2-52 (300)
98 KOG4275 Predicted E3 ubiquitin 71.8 2.5 5.4E-05 43.5 2.1 28 116-145 300-328 (350)
99 PF10367 Vps39_2: Vacuolar sor 70.4 1.8 4E-05 37.5 0.7 32 115-146 77-108 (109)
100 KOG3039 Uncharacterized conser 70.0 2.5 5.4E-05 42.5 1.6 53 115-177 220-274 (303)
101 PLN03086 PRLI-interacting fact 69.5 9.6 0.00021 43.3 6.3 57 159-238 406-463 (567)
102 PF00643 zf-B_box: B-box zinc 69.5 3.9 8.5E-05 29.3 2.2 33 277-316 4-38 (42)
103 PF09297 zf-NADH-PPase: NADH p 69.2 6.2 0.00013 26.9 3.0 28 275-302 2-30 (32)
104 PF15227 zf-C3HC4_4: zinc fing 68.7 2.5 5.4E-05 30.8 1.0 28 279-311 1-28 (42)
105 COG5175 MOT2 Transcriptional r 68.4 2 4.4E-05 44.9 0.6 52 116-176 14-67 (480)
106 KOG1952 Transcription factor N 67.8 3.6 7.7E-05 48.1 2.5 50 115-165 190-241 (950)
107 smart00546 CUE Domain that may 67.3 20 0.00042 26.0 5.6 38 52-89 3-41 (43)
108 cd00194 UBA Ubiquitin Associat 67.1 18 0.00039 25.2 5.2 34 54-88 4-37 (38)
109 PF14835 zf-RING_6: zf-RING of 67.1 3.1 6.8E-05 33.3 1.3 34 277-310 8-49 (65)
110 KOG3002 Zn finger protein [Gen 66.6 7.7 0.00017 40.7 4.5 87 113-232 45-132 (299)
111 COG5222 Uncharacterized conser 66.6 3.7 8E-05 42.3 2.1 43 117-170 275-318 (427)
112 PF13719 zinc_ribbon_5: zinc-r 66.4 5.8 0.00013 28.1 2.5 28 208-238 3-35 (37)
113 PF05320 Pox_RNA_Pol_19: Poxvi 66.4 2.4 5.3E-05 39.5 0.7 9 116-124 126-134 (167)
114 PF13717 zinc_ribbon_4: zinc-r 66.0 5.9 0.00013 27.9 2.4 28 208-238 3-35 (36)
115 PHA03096 p28-like protein; Pro 65.8 3.2 6.8E-05 43.2 1.5 37 117-153 179-221 (284)
116 PRK00398 rpoP DNA-directed RNA 65.4 5.5 0.00012 29.5 2.3 29 277-305 4-33 (46)
117 smart00165 UBA Ubiquitin assoc 65.0 17 0.00037 25.2 4.7 33 54-87 4-36 (37)
118 KOG3579 Predicted E3 ubiquitin 64.4 5.3 0.00011 41.0 2.7 54 114-170 266-322 (352)
119 TIGR00622 ssl1 transcription f 64.2 3.9 8.4E-05 36.5 1.5 38 208-248 56-101 (112)
120 cd00021 BBOX B-Box-type zinc f 63.1 6 0.00013 27.6 2.1 31 278-315 2-34 (39)
121 KOG2807 RNA polymerase II tran 61.6 3.6 7.7E-05 43.0 0.9 85 137-248 275-365 (378)
122 cd07666 BAR_SNX7 The Bin/Amphi 61.5 1.9E+02 0.0041 29.5 13.3 99 383-492 140-238 (243)
123 KOG1941 Acetylcholine receptor 60.4 16 0.00036 39.2 5.5 48 115-170 364-413 (518)
124 KOG2177 Predicted E3 ubiquitin 60.2 4.7 0.0001 40.7 1.5 24 278-308 88-112 (386)
125 PF02150 RNA_POL_M_15KD: RNA p 59.0 6.6 0.00014 27.5 1.6 27 208-237 2-29 (35)
126 PRK14559 putative protein seri 58.7 7 0.00015 45.3 2.7 12 276-287 41-52 (645)
127 PRK08665 ribonucleotide-diphos 58.3 5.2 0.00011 47.3 1.7 26 277-304 725-751 (752)
128 PF14447 Prok-RING_4: Prokaryo 58.3 4.1 8.9E-05 31.6 0.5 44 116-173 7-50 (55)
129 cd07630 BAR_SNX_like The Bin/A 57.3 83 0.0018 31.0 9.7 99 384-492 95-193 (198)
130 KOG0320 Predicted E3 ubiquitin 57.0 2.6 5.6E-05 40.5 -0.9 29 233-287 150-178 (187)
131 PF14812 PBP1_TM: Transmembran 56.8 3.6 7.8E-05 34.5 0.0 12 9-20 36-47 (81)
132 PF08938 HBS1_N: HBS1 N-termin 56.8 1.3 2.8E-05 37.0 -2.7 47 42-89 20-69 (79)
133 PF08274 PhnA_Zn_Ribbon: PhnA 56.7 9 0.0002 26.0 1.9 26 277-303 3-29 (30)
134 KOG2906 RNA polymerase III sub 55.6 8.3 0.00018 33.4 2.0 28 278-305 3-33 (105)
135 PF07191 zinc-ribbons_6: zinc- 55.3 10 0.00022 31.0 2.3 32 278-311 3-40 (70)
136 PLN03208 E3 ubiquitin-protein 55.0 4.1 8.8E-05 39.9 0.0 32 276-312 18-49 (193)
137 TIGR02098 MJ0042_CXXC MJ0042 f 54.8 13 0.00028 26.1 2.7 27 209-238 4-35 (38)
138 PRK04023 DNA polymerase II lar 54.0 10 0.00022 45.5 3.0 35 201-245 620-660 (1121)
139 KOG3970 Predicted E3 ubiquitin 53.9 9 0.0002 38.1 2.2 54 117-172 51-104 (299)
140 KOG1493 Anaphase-promoting com 53.9 3.3 7.1E-05 34.2 -0.7 48 118-172 22-80 (84)
141 COG1998 RPS31 Ribosomal protei 53.7 9.3 0.0002 28.9 1.7 26 276-301 19-45 (51)
142 KOG0978 E3 ubiquitin ligase in 53.1 4 8.8E-05 47.2 -0.4 30 233-287 660-689 (698)
143 PF07282 OrfB_Zn_ribbon: Putat 52.8 12 0.00025 30.0 2.4 28 275-302 27-55 (69)
144 COG5219 Uncharacterized conser 52.5 6.2 0.00013 46.7 1.0 52 114-173 1467-1523(1525)
145 PRK05654 acetyl-CoA carboxylas 52.2 3.6 7.8E-05 43.0 -0.9 28 276-303 27-56 (292)
146 PF10168 Nup88: Nuclear pore c 51.7 4.8E+02 0.01 31.0 16.7 48 432-480 601-648 (717)
147 COG1198 PriA Primosomal protei 51.5 11 0.00024 44.2 2.9 34 277-310 445-484 (730)
148 PF14369 zf-RING_3: zinc-finge 50.0 14 0.00031 25.9 2.1 28 208-238 3-31 (35)
149 COG1645 Uncharacterized Zn-fin 49.9 11 0.00023 34.6 1.9 24 276-308 28-51 (131)
150 PF09538 FYDLN_acid: Protein o 49.5 9.2 0.0002 34.0 1.4 25 277-303 10-36 (108)
151 smart00336 BBOX B-Box-type zin 49.2 16 0.00034 25.8 2.4 33 277-316 4-38 (42)
152 COG2888 Predicted Zn-ribbon RN 47.3 12 0.00026 29.4 1.6 6 278-283 29-34 (61)
153 KOG1571 Predicted E3 ubiquitin 47.2 10 0.00023 40.3 1.6 44 114-172 303-346 (355)
154 KOG2034 Vacuolar sorting prote 47.2 9.9 0.00022 44.8 1.6 38 115-152 816-853 (911)
155 PRK14714 DNA polymerase II lar 46.8 15 0.00032 45.2 3.0 29 472-500 846-881 (1337)
156 KOG3161 Predicted E3 ubiquitin 46.8 7 0.00015 44.4 0.2 36 116-151 11-48 (861)
157 PF06677 Auto_anti-p27: Sjogre 46.7 16 0.00035 26.6 2.1 22 277-300 18-41 (41)
158 KOG1940 Zn-finger protein [Gen 46.4 15 0.00033 38.0 2.6 47 114-170 156-204 (276)
159 TIGR00595 priA primosomal prot 46.3 17 0.00037 41.0 3.3 34 277-310 223-262 (505)
160 KOG3039 Uncharacterized conser 46.2 13 0.00027 37.6 1.9 37 117-155 44-80 (303)
161 PF14445 Prok-RING_2: Prokaryo 45.9 4.8 0.0001 30.5 -0.8 33 115-147 6-39 (57)
162 cd07621 BAR_SNX5_6 The Bin/Amp 45.6 1.5E+02 0.0032 29.8 9.4 60 436-495 156-215 (219)
163 CHL00174 accD acetyl-CoA carbo 45.2 5 0.00011 41.9 -1.1 27 277-303 39-67 (296)
164 PF12906 RINGv: RING-variant d 45.2 19 0.00041 26.9 2.3 33 119-151 1-38 (47)
165 PRK14714 DNA polymerase II lar 44.4 15 0.00032 45.2 2.5 56 440-496 799-858 (1337)
166 PRK00398 rpoP DNA-directed RNA 43.9 25 0.00055 25.9 2.8 29 209-241 5-34 (46)
167 COG5432 RAD18 RING-finger-cont 43.8 10 0.00022 39.1 0.8 32 277-315 26-59 (391)
168 PF13834 DUF4193: Domain of un 43.7 10 0.00023 33.0 0.8 32 113-144 67-98 (99)
169 KOG2932 E3 ubiquitin ligase in 43.6 8.3 0.00018 40.1 0.2 53 204-292 87-139 (389)
170 PF10446 DUF2457: Protein of u 43.5 16 0.00034 40.0 2.3 21 107-127 185-205 (458)
171 TIGR00515 accD acetyl-CoA carb 43.3 5.8 0.00013 41.3 -1.0 28 276-303 26-55 (285)
172 PF10446 DUF2457: Protein of u 43.2 13 0.00027 40.7 1.5 6 346-351 407-412 (458)
173 smart00661 RPOL9 RNA polymeras 43.2 21 0.00046 26.7 2.4 27 208-237 1-29 (52)
174 PF02318 FYVE_2: FYVE-type zin 42.9 39 0.00084 30.3 4.4 42 275-317 53-95 (118)
175 TIGR03655 anti_R_Lar restricti 42.7 21 0.00046 27.2 2.3 11 277-287 2-12 (53)
176 PRK14873 primosome assembly pr 42.3 19 0.00042 42.0 3.0 34 277-310 393-431 (665)
177 cd07662 BAR_SNX6 The Bin/Amphi 41.8 1.6E+02 0.0034 29.6 8.8 62 432-493 149-212 (218)
178 KOG3268 Predicted E3 ubiquitin 41.7 23 0.00049 34.1 2.7 57 115-173 164-228 (234)
179 COG5574 PEX10 RING-finger-cont 41.6 7.2 0.00016 39.8 -0.6 36 115-150 94-132 (271)
180 PF12773 DZR: Double zinc ribb 41.4 11 0.00023 28.2 0.4 12 277-288 30-41 (50)
181 KOG4362 Transcriptional regula 41.3 7.2 0.00016 45.0 -0.7 50 116-174 21-70 (684)
182 TIGR01384 TFS_arch transcripti 41.1 18 0.00039 31.5 1.9 24 277-302 1-25 (104)
183 PF14569 zf-UDP: Zinc-binding 41.1 13 0.00029 30.8 1.0 54 215-293 14-68 (80)
184 COG1997 RPL43A Ribosomal prote 41.0 23 0.00049 30.2 2.4 29 276-304 35-64 (89)
185 KOG0309 Conserved WD40 repeat- 40.9 19 0.00041 41.8 2.5 47 115-170 1027-1073(1081)
186 KOG2114 Vacuolar assembly/sort 40.5 18 0.00038 42.6 2.2 40 117-170 841-880 (933)
187 PF04931 DNA_pol_phi: DNA poly 40.1 53 0.0012 39.2 6.3 20 68-87 764-783 (784)
188 PF07975 C1_4: TFIIH C1-like d 39.1 12 0.00027 28.6 0.5 22 228-249 20-42 (51)
189 PF01363 FYVE: FYVE zinc finge 39.1 18 0.00038 28.9 1.5 37 114-150 7-45 (69)
190 PF03943 TAP_C: TAP C-terminal 37.7 39 0.00084 25.7 3.0 37 53-89 2-38 (51)
191 smart00804 TAP_C C-terminal do 37.7 1.3E+02 0.0028 24.1 6.1 41 49-89 10-50 (63)
192 PF09026 CENP-B_dimeris: Centr 37.7 11 0.00024 32.6 0.0 10 53-62 51-60 (101)
193 PRK05580 primosome assembly pr 37.7 27 0.00058 41.0 3.2 34 277-310 391-430 (679)
194 PF08580 KAR9: Yeast cortical 37.7 3.7E+02 0.0079 31.8 12.3 63 434-496 272-338 (683)
195 KOG0943 Predicted ubiquitin-pr 37.3 19 0.0004 43.9 1.7 17 436-452 2419-2435(3015)
196 PHA02926 zinc finger-like prot 37.1 11 0.00023 37.7 -0.2 35 233-287 196-230 (242)
197 PF14446 Prok-RING_1: Prokaryo 37.0 26 0.00056 27.2 1.9 32 116-147 5-38 (54)
198 PRK14892 putative transcriptio 36.9 25 0.00054 30.8 2.1 27 276-302 21-51 (99)
199 PF02891 zf-MIZ: MIZ/SP-RING z 36.7 35 0.00075 25.9 2.6 46 117-170 3-49 (50)
200 PF12959 DUF3848: Protein of u 36.1 1.4E+02 0.003 26.2 6.5 48 42-90 24-76 (101)
201 PRK12495 hypothetical protein; 36.1 39 0.00084 33.7 3.5 18 275-292 41-58 (226)
202 PF06827 zf-FPG_IleRS: Zinc fi 35.7 26 0.00056 23.3 1.6 24 277-300 2-28 (30)
203 PF01599 Ribosomal_S27: Riboso 35.6 28 0.00061 26.2 1.9 26 276-301 18-46 (47)
204 COG0777 AccD Acetyl-CoA carbox 34.5 13 0.00028 38.2 -0.0 28 276-303 28-57 (294)
205 PF08746 zf-RING-like: RING-li 34.5 29 0.00063 25.4 1.8 41 119-165 1-42 (43)
206 TIGR00686 phnA alkylphosphonat 34.2 29 0.00063 30.7 2.1 26 277-303 3-29 (109)
207 PF14803 Nudix_N_2: Nudix N-te 34.1 34 0.00075 23.9 2.0 27 208-237 1-31 (34)
208 KOG2164 Predicted E3 ubiquitin 33.7 16 0.00034 40.7 0.4 28 276-310 186-215 (513)
209 PF05290 Baculo_IE-1: Baculovi 33.6 24 0.00053 32.4 1.6 51 115-172 79-131 (140)
210 PRK11827 hypothetical protein; 32.6 38 0.00083 26.9 2.3 25 277-301 9-34 (60)
211 PRK14811 formamidopyrimidine-D 32.5 30 0.00065 35.7 2.3 25 276-300 235-262 (269)
212 PF03119 DNA_ligase_ZBD: NAD-d 32.2 40 0.00088 22.4 2.0 20 278-297 1-20 (28)
213 COG0266 Nei Formamidopyrimidin 31.5 32 0.00069 35.6 2.2 25 276-300 245-272 (273)
214 COG1623 Predicted nucleic-acid 31.5 1.6E+02 0.0036 30.8 7.2 31 334-364 151-181 (349)
215 COG5236 Uncharacterized conser 31.3 28 0.00061 36.8 1.8 32 114-147 59-90 (493)
216 PF04899 MbeD_MobD: MbeD/MobD 31.3 2.9E+02 0.0064 22.6 7.6 45 435-484 18-62 (70)
217 PHA02929 N1R/p28-like protein; 31.2 20 0.00044 36.3 0.7 38 276-313 174-214 (238)
218 PRK09710 lar restriction allev 31.1 44 0.00095 26.8 2.4 14 275-288 5-18 (64)
219 PRK01103 formamidopyrimidine/5 31.1 33 0.00072 35.4 2.3 25 276-300 245-272 (274)
220 COG3416 Uncharacterized protei 30.6 1.8E+02 0.0038 29.0 6.9 61 466-531 57-122 (233)
221 COG5109 Uncharacterized conser 30.5 41 0.00089 35.2 2.8 50 115-171 335-385 (396)
222 TIGR00577 fpg formamidopyrimid 30.5 35 0.00075 35.3 2.3 24 277-300 246-272 (272)
223 PF08792 A2L_zn_ribbon: A2L zi 30.2 54 0.0012 22.7 2.5 12 276-287 3-14 (33)
224 KOG0943 Predicted ubiquitin-pr 30.0 26 0.00057 42.8 1.4 8 280-287 2282-2289(3015)
225 PRK14810 formamidopyrimidine-D 30.0 35 0.00076 35.3 2.2 25 276-300 244-271 (272)
226 PRK13945 formamidopyrimidine-D 29.8 35 0.00077 35.4 2.3 25 276-300 254-281 (282)
227 PF12861 zf-Apc11: Anaphase-pr 29.4 20 0.00043 30.5 0.3 35 277-314 33-67 (85)
228 PRK10445 endonuclease VIII; Pr 28.6 40 0.00086 34.7 2.3 25 276-300 235-262 (263)
229 COG5151 SSL1 RNA polymerase II 28.1 18 0.0004 37.6 -0.2 89 137-248 307-408 (421)
230 PRK04023 DNA polymerase II lar 27.9 38 0.00082 40.9 2.2 31 274-310 624-660 (1121)
231 PF15290 Syntaphilin: Golgi-lo 27.8 3.8E+02 0.0083 27.9 9.0 20 468-487 121-140 (305)
232 KOG3053 Uncharacterized conser 27.3 43 0.00094 34.1 2.2 53 115-170 19-79 (293)
233 TIGR02300 FYDLN_acid conserved 27.3 35 0.00075 31.2 1.4 26 277-303 10-36 (129)
234 PF07800 DUF1644: Protein of u 27.2 59 0.0013 30.9 3.0 36 116-153 2-50 (162)
235 PLN02189 cellulose synthase 26.9 38 0.00083 41.1 2.1 60 209-296 36-96 (1040)
236 KOG4684 Uncharacterized conser 26.8 63 0.0014 32.1 3.2 16 208-224 139-154 (275)
237 PRK10220 hypothetical protein; 26.4 49 0.0011 29.4 2.1 26 277-303 4-30 (111)
238 PF12677 DUF3797: Domain of un 26.4 58 0.0013 24.7 2.2 28 276-303 13-48 (49)
239 PF10267 Tmemb_cc2: Predicted 26.3 3.1E+02 0.0067 30.1 8.7 25 431-455 48-72 (395)
240 COG1594 RPB9 DNA-directed RNA 25.7 52 0.0011 29.4 2.3 27 277-303 3-32 (113)
241 KOG0825 PHD Zn-finger protein 25.5 47 0.001 38.9 2.3 48 116-173 123-171 (1134)
242 TIGR01206 lysW lysine biosynth 24.7 80 0.0017 24.5 2.8 27 209-238 4-32 (54)
243 PF14471 DUF4428: Domain of un 24.2 55 0.0012 25.0 1.8 30 118-148 1-30 (51)
244 cd07622 BAR_SNX4 The Bin/Amphi 24.1 6.9E+02 0.015 24.5 15.1 97 382-492 98-194 (201)
245 PF10122 Mu-like_Com: Mu-like 24.1 33 0.00072 26.2 0.6 25 277-301 5-32 (51)
246 PF06906 DUF1272: Protein of u 24.0 27 0.00058 27.2 0.1 44 117-172 6-51 (57)
247 PF14149 YhfH: YhfH-like prote 23.8 6.3 0.00014 28.1 -3.1 26 274-299 11-37 (37)
248 COG5175 MOT2 Transcriptional r 23.6 15 0.00034 38.6 -1.7 30 209-243 16-45 (480)
249 PRK09521 exosome complex RNA-b 23.5 55 0.0012 31.8 2.2 25 278-303 151-176 (189)
250 PF13453 zf-TFIIB: Transcripti 23.4 57 0.0012 23.4 1.7 29 278-311 1-29 (41)
251 PLN02638 cellulose synthase A 23.4 45 0.00098 40.7 1.8 57 215-296 22-79 (1079)
252 TIGR00373 conserved hypothetic 23.4 95 0.0021 29.4 3.7 32 203-237 105-137 (158)
253 KOG0801 Predicted E3 ubiquitin 23.3 28 0.0006 33.0 0.1 29 114-142 175-204 (205)
254 PF06844 DUF1244: Protein of u 22.9 49 0.0011 26.7 1.4 18 139-156 11-28 (68)
255 PRK12775 putative trifunctiona 22.5 1.1E+03 0.023 29.3 13.4 15 276-290 796-810 (1006)
256 TIGR00993 3a0901s04IAP86 chlor 22.4 1.1E+02 0.0023 36.0 4.4 40 39-82 413-452 (763)
257 PF01428 zf-AN1: AN1-like Zinc 22.2 53 0.0011 23.9 1.4 26 214-245 4-30 (43)
258 KOG4759 Ribosome recycling fac 22.0 6.5E+02 0.014 26.0 9.4 66 432-497 197-262 (263)
259 smart00531 TFIIE Transcription 22.0 1.2E+02 0.0026 28.2 4.1 19 56-74 19-37 (147)
260 PF03615 GCM: GCM motif protei 21.8 79 0.0017 29.1 2.6 21 277-303 83-107 (143)
261 smart00659 RPOLCX RNA polymera 21.6 79 0.0017 23.4 2.2 10 277-286 20-29 (44)
262 COG1096 Predicted RNA-binding 21.5 60 0.0013 31.6 1.9 24 277-302 150-174 (188)
263 PRK04778 septation ring format 21.5 1.1E+03 0.024 26.9 12.6 78 401-499 154-232 (569)
264 PLN02436 cellulose synthase A 21.2 57 0.0012 39.8 2.1 57 215-296 41-98 (1094)
265 PRK08115 ribonucleotide-diphos 21.2 45 0.00097 40.0 1.2 24 277-302 828-853 (858)
266 PF15358 TSKS: Testis-specific 21.1 6.8E+02 0.015 27.5 9.7 90 339-457 123-214 (558)
267 KOG2906 RNA polymerase III sub 21.0 96 0.0021 27.1 2.8 28 208-238 2-31 (105)
268 PF06044 DRP: Dam-replacing fa 20.9 71 0.0015 32.5 2.4 35 268-303 24-63 (254)
269 PHA02664 hypothetical protein; 20.8 1.3E+02 0.0028 31.7 4.3 13 51-63 521-533 (534)
270 KOG2856 Adaptor protein PACSIN 20.7 1.1E+03 0.024 25.6 14.5 26 430-455 216-241 (472)
271 PRK06266 transcription initiat 20.7 1.1E+02 0.0024 29.6 3.6 32 203-237 113-145 (178)
272 KOG0804 Cytoplasmic Zn-finger 20.5 1.2E+03 0.026 26.0 12.7 28 542-571 465-492 (493)
273 PRK12286 rpmF 50S ribosomal pr 20.5 60 0.0013 25.4 1.4 13 275-287 26-38 (57)
274 TIGR02443 conserved hypothetic 20.4 92 0.002 24.6 2.4 26 278-303 11-41 (59)
275 COG2051 RPS27A Ribosomal prote 20.4 1.1E+02 0.0023 24.8 2.8 31 208-241 20-51 (67)
276 KOG3970 Predicted E3 ubiquitin 20.3 42 0.00092 33.5 0.6 80 236-329 21-101 (299)
277 PF05605 zf-Di19: Drought indu 20.3 1.3E+02 0.0029 22.8 3.3 45 116-177 2-46 (54)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-67 Score=575.28 Aligned_cols=429 Identities=40% Similarity=0.765 Sum_probs=381.4
Q ss_pred eeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhcChhhhhHhhCCcccCCCCCCCCcccccccc
Q 007785 41 VITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPMLPLSSTVMCD 120 (590)
Q Consensus 41 vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~C~ 120 (590)
|+|.+++...|.++|.+|+++|+++..+|++||.||.|+.+++++.|++ +.+.++...|+.... .......|.
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~------~~~~~~~c~ 74 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWP------KKKGDVQCG 74 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccC------CCCccccCC
Confidence 6889999999999999999999999999999999999999999999996 556777778865443 234568999
Q ss_pred cccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCc-hHHHHHHHHHhhh
Q 007785 121 ICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHP-NLAEKFERFLLES 199 (590)
Q Consensus 121 IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~-e~~eky~~~l~~~ 199 (590)
||++.++. .+..+.|||.||..||..|+..+|.+|....|+||..+|.+.+....|..+++ + +...+|.++++.+
T Consensus 75 ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s---~~~~~~ky~~~i~~s 150 (444)
T KOG1815|consen 75 ICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVS---DKEDKEKYQRYILRS 150 (444)
T ss_pred cccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecC---CHHHHHHHHHHHHHH
Confidence 99999775 67788999999999999999999998875559999999999999999999998 5 5899999999999
Q ss_pred hhhcCcccccCCCCCCCCceEeecCcccceeeccCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCC
Q 007785 200 FIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPC 279 (590)
Q Consensus 200 ~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~C 279 (590)
||+.+..++|||+ |+|++++.........|.|.||+.|||.|+.+||.|++|..+..|.++..+++++.+||..|+++|
T Consensus 151 yve~~~~lkwCP~-~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~C 229 (444)
T KOG1815|consen 151 YVEDNVPLKWCPA-PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKEC 229 (444)
T ss_pred HHhcCCccccCCC-CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccC
Confidence 9999999999995 999999997555556799999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeecCCCCeeEec---cCceeeccccccccCCCcccccCCcccCCcchhHHHH-HHHHHHHHHHHHHHHHHHHH
Q 007785 280 PKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKK-TERAKRELYRYMHYHNRYKA 355 (590)
Q Consensus 280 PkC~~~IEKn~GCNHMtC~---Cg~~FCwlC~~~~~~~H~w~~~~g~~C~~y~~~~~~~-~~~~k~~l~ry~~y~~r~~~ 355 (590)
|+|..+|||++|||||+|. |++.|||+|++.|.. |+.++ ++.||+|..+.... +..++..+.||.|||.||+.
T Consensus 230 P~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~-h~~~~--~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~~ 306 (444)
T KOG1815|consen 230 PKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSD-HGSST--GYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWME 306 (444)
T ss_pred CCcccchhccCCccccccccCCcCCeeceeeeccccc-ccccc--eeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHHh
Confidence 9999999999999999994 999999999888753 44333 79999999877655 78888999999999999999
Q ss_pred hhhhHHHHHHHHHHHHHH-HHHHhhh-hccccchHHHHHHHHHHHHHHHhhhccccceeecccccchhcccchHHHHHHH
Q 007785 356 HTDSFKLESKLKETVLEK-VSISEER-ESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQ 433 (590)
Q Consensus 356 h~~s~k~e~~l~~~i~~k-~~~~~~~-~~~~~~~~~l~~a~~~l~~~R~vL~~SY~~ayy~~~~~~~~~~~~~~~~~~~~ 433 (590)
|..+++++..+...+.+. ...+... ...+.+++|+.+|+.+|+++|++|+|||+|+||+... .+.
T Consensus 307 ~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~~-------------~~~ 373 (444)
T KOG1815|consen 307 HQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSEN-------------NKR 373 (444)
T ss_pred hhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhccc-------------chh
Confidence 999999998877766544 3333222 2347799999999999999999999999999999732 344
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 007785 434 HLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLG 497 (590)
Q Consensus 434 ~lfe~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~ 497 (590)
++||++|.+|+..+|.|+..++.++...+.+++..+|+++.+++.++++++.++++.++++|-.
T Consensus 374 ~~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 437 (444)
T KOG1815|consen 374 NLFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLED 437 (444)
T ss_pred hhhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccchhhhhHHHHHHHHHHhcccc
Confidence 8999999999999999999999988877778899999999999999999999999999988863
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-34 Score=304.49 Aligned_cols=223 Identities=32% Similarity=0.681 Sum_probs=184.7
Q ss_pred cccccccccccc-cccCcee-cCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHH
Q 007785 115 STVMCDICMEEV-AGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKF 192 (590)
Q Consensus 115 ~~~~C~IC~e~~-~~~~~~~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 192 (590)
...+|.||+.+. ....++. ..|+|.||.+||++|+..+...| ..++||..+|+..++.+....+|+ +.+.++|
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 467999999543 3335554 48999999999999999985444 479999999999999999999999 8899999
Q ss_pred HHHHhhhhhhcCcccccCCCCCCCCceEeecC----cccceeecc-CCCeeecCccCcCCCCCCchhhHHHHHhhhchHH
Q 007785 193 ERFLLESFIEDNKMVKWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESE 267 (590)
Q Consensus 193 ~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~----~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e 267 (590)
++++.+.++.....+ +|| .|+|...+.... .......|+ |+..||..|+.+||.+.+|..+++|......+..
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 699998776433 223334675 9999999999999999999999999987778888
Q ss_pred hHHHHHhCCcCCCCCCcceeecCCCCeeEeccCceeeccccccccCCCcccccCCcccCCcchhHHHHHHHHHHHHHHHH
Q 007785 268 TVNWITVHTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKKTERAKRELYRYM 347 (590)
Q Consensus 268 ~~~~i~~~tK~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~~~~H~w~~~~g~~C~~y~~~~~~~~~~~k~~l~ry~ 347 (590)
+++++..+|++||+|+..|++++|||||+|+||++|||.|+++|.... +.-+.|.++... .
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 899999999999999999999999999999999999999999963211 112456666653 6
Q ss_pred HHHHHHHHhhhhHHHH
Q 007785 348 HYHNRYKAHTDSFKLE 363 (590)
Q Consensus 348 ~y~~r~~~h~~s~k~e 363 (590)
+|+.++.+|.....++
T Consensus 359 ~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 359 HYFEDDENHDKSIQLE 374 (384)
T ss_pred cccccccccccccccc
Confidence 7777777776665544
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-33 Score=290.22 Aligned_cols=205 Identities=27% Similarity=0.666 Sum_probs=175.8
Q ss_pred ccccccccccccccc-cCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHH
Q 007785 114 SSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKF 192 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~-~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 192 (590)
...+.|.|||+.... ..+..++|+|.||+.|++.|++..|++|.+..++||.++|+...++..++.+|. .++++||
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg---~EL~arY 258 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVG---DELFARY 258 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHH---HHHHHHH
Confidence 356899999999776 456778999999999999999999999999999999999999999999999999 9999999
Q ss_pred HHHHhhhhhhcCcccccCCCCCCCCceEeecCcccceeecc-CCCeeecCccCcCCCCCCchhh--------HHHHH---
Q 007785 193 ERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMW--------DLWAK--- 260 (590)
Q Consensus 193 ~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~--------~~w~~--- 260 (590)
++.++++.++...++++|| .+.|+.++. .+.....+.|+ |..+||+.|+..||...+|... ..|..
T Consensus 259 e~l~lqk~l~~msdv~yCP-r~~Cq~p~~-~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCP-RACCQLPVK-QDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE 336 (445)
T ss_pred HHHHHHHHHHhhcccccCC-hhhccCccc-cCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence 9999999999999999999 689999884 44444568996 9999999999999999999643 22221
Q ss_pred ----------------hhhchHHhHHHHHhCCcCCCCCCcceeecCCCCeeEe-ccCceeeccccccccCCCcccccCCc
Q 007785 261 ----------------KCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTWSRIAGH 323 (590)
Q Consensus 261 ----------------~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~~~H~w~~~~g~ 323 (590)
...++-.+.+|+..|.|+||+|+++|||++|||||+| .|++.|||+|.....+..+|.|+.+.
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 1112334568999999999999999999999999999 69999999999987777667766543
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=1.7e-24 Score=215.24 Aligned_cols=197 Identities=29% Similarity=0.655 Sum_probs=149.0
Q ss_pred cccccccccccccccccCceecCCC--CccchhhHHHHHHhhhhcCCc-------ccccccccccccccc-hHHHHHHhc
Q 007785 113 LSSTVMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQS-------KRIRCMAHKCNAICD-EAVVRNLVS 182 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~FC~~C~~~yi~~~I~~g~~-------~~i~CP~~~C~~~~~-~~~i~~ll~ 182 (590)
++...+|..|.+.-+ .+..++|. |..|.+|++.|..+.+++.++ ..+.||. +|...+- +-.--++|.
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 NSRNITCITCTDVRS--PVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCcc--ceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 457789999988733 55566888 999999999999999987653 2356664 5665432 222235677
Q ss_pred CCCchHHHHHHHHHhhhhhhcCcccccCCCCCCCCceEeecCcccceeecc--CCCeeecCccCcCCCC-C---------
Q 007785 183 KKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA--CGAQFCFSCLSEAHSP-C--------- 250 (590)
Q Consensus 183 ~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--Cg~~fC~~C~~~~H~p-~--------- 250 (590)
.+.+.+|+++..+.+|.....+ -|| .|+|+..+..+++. ..|+|+ ||..||..|.+.+|.+ +
T Consensus 295 ---~e~Y~rYQr~atEe~vlq~gGV-lCP-~pgCG~gll~EPD~-rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t 368 (446)
T KOG0006|consen 295 ---EEQYNRYQRYATEECVLQMGGV-LCP-RPGCGAGLLPEPDQ-RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGT 368 (446)
T ss_pred ---hhHHHHHHHhhhhhheeecCCE-ecC-CCCCCcccccCCCC-CcccCCCCchhHhHHHHHhhhccccceeeeccccc
Confidence 8999999999999999888765 799 79999998877754 358994 9999999999999975 1
Q ss_pred -Cchhh--HHHHHhhhchHHhHHHHHhCCcCCCCCCcceeecCCCCeeEe-c--cCceeeccccccccCCCccc
Q 007785 251 -SCSMW--DLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-I--CGQAFCWLCGGATGRDHTWS 318 (590)
Q Consensus 251 -sC~~~--~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCNHMtC-~--Cg~~FCwlC~~~~~~~H~w~ 318 (590)
+|... ..-....+-+..+..-|+..||+||+|+.|.||||||+||.| + ||.+|||.|+-.|.+.-.|.
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~Cmgd 442 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGD 442 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccc
Confidence 24310 000011122334445578899999999999999999999999 4 99999999999998754443
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.18 E-value=3.2e-11 Score=96.24 Aligned_cols=62 Identities=53% Similarity=1.092 Sum_probs=55.2
Q ss_pred HHHHHHHhhhhhhcCcccccCCCCCCCCceEeec-Ccccceeec-cCCCeeecCccCcCCCCCCc
Q 007785 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE-EVEVCEVEC-ACGAQFCFSCLSEAHSPCSC 252 (590)
Q Consensus 190 eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C-~Cg~~fC~~C~~~~H~p~sC 252 (590)
++|++++++++|+.++.++||| +|+|+.++... +.....|.| .|+..||+.|+.+||.|.+|
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 79999999976 345567999 59999999999999999987
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=99.09 E-value=3.6e-11 Score=95.85 Aligned_cols=62 Identities=35% Similarity=0.960 Sum_probs=42.6
Q ss_pred HHHHHHHhhhhhhcCcccccCCCCCCCCceEeecCcccc-eeecc-CCCeeecCccCcCCCCCCc
Q 007785 190 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVC-EVECA-CGAQFCFSCLSEAHSPCSC 252 (590)
Q Consensus 190 eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-Cg~~fC~~C~~~~H~p~sC 252 (590)
++|++++++.+|+.++.++||| +|+|+.++........ .++|+ |++.||+.|+.+||.|.+|
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 5789999999999888999999 6999999997775444 38997 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=98.52 E-value=4.2e-08 Score=71.95 Aligned_cols=41 Identities=24% Similarity=0.741 Sum_probs=30.4
Q ss_pred cccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
|+||++.+. ++++++|||.||..|+..++...-.. .+.||.
T Consensus 1 CpiC~~~~~--~Pv~l~CGH~FC~~Cl~~~~~~~~~~----~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFK--DPVSLPCGHSFCRSCLERLWKEPSGS----GFSCPE 41 (42)
T ss_dssp ETTTTSB-S--SEEE-SSSSEEEHHHHHHHHCCSSSS----T---SS
T ss_pred CCccchhhC--CccccCCcCHHHHHHHHHHHHccCCc----CCCCcC
Confidence 899999977 99999999999999999999763222 278986
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=98.14 E-value=1.3e-06 Score=62.92 Aligned_cols=37 Identities=30% Similarity=0.872 Sum_probs=29.4
Q ss_pred cccccccccccCc-eecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 119 CDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 119 C~IC~e~~~~~~~-~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
|+||++.+. ++ +.++|||.||.+||..|+... .+||.
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 899999866 56 577999999999999998762 47876
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=98.11 E-value=1.4e-06 Score=64.32 Aligned_cols=40 Identities=38% Similarity=0.836 Sum_probs=33.0
Q ss_pred cccccccccc-ccCceecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 118 MCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 118 ~C~IC~e~~~-~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
+|+||++++. ...++.++|||.||.+|+..|+... .+||.
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 4567788999999999999999762 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=98.10 E-value=2.1e-06 Score=62.26 Aligned_cols=39 Identities=31% Similarity=0.867 Sum_probs=32.3
Q ss_pred cccccccccccCce-ecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 119 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 119 C~IC~e~~~~~~~~-~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
|+||++.+. .+. .++|||.||..||.+++.. . ..++||.
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 899999866 555 7799999999999999997 2 2468986
No 11
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.00 E-value=8.4e-06 Score=64.75 Aligned_cols=38 Identities=37% Similarity=0.872 Sum_probs=34.4
Q ss_pred CCcCCC--CCCcceeecC--CCCeeEe-ccCceeecccccccc
Q 007785 275 HTKPCP--KCHKPVEKNG--GCNLVSC-ICGQAFCWLCGGATG 312 (590)
Q Consensus 275 ~tK~CP--kC~~~IEKn~--GCNHMtC-~Cg~~FCwlC~~~~~ 312 (590)
+.+.|| +|...|+... |.++|+| .|++.|||.|+.+||
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 568899 9999999964 9999999 799999999999974
No 12
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=3.3e-06 Score=79.55 Aligned_cols=53 Identities=25% Similarity=0.662 Sum_probs=42.2
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~ 176 (590)
...+.|+||++.+....+++..|||.||..|++.-+.. .-+||. |...++...
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~ 181 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQ 181 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhh
Confidence 45689999999998777888999999999999987764 248999 554554433
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.98 E-value=4.9e-06 Score=80.30 Aligned_cols=64 Identities=23% Similarity=0.537 Sum_probs=47.1
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhc--------CCcccccccccccccccchHHHHHHh
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE--------GQSKRIRCMAHKCNAICDEAVVRNLV 181 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~--------g~~~~i~CP~~~C~~~~~~~~i~~ll 181 (590)
.+.++|+||++.+. +++.++|||.||..|+..|+...-.. ......+||. |+..+....+..+.
T Consensus 16 ~~~~~CpICld~~~--dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy 87 (193)
T PLN03208 16 GGDFDCNICLDQVR--DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY 87 (193)
T ss_pred CCccCCccCCCcCC--CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence 45689999999865 78888999999999999997642110 0113579999 99988765554444
No 14
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.94 E-value=5.1e-06 Score=61.15 Aligned_cols=41 Identities=32% Similarity=0.783 Sum_probs=23.1
Q ss_pred cccccccccc--cCceecCCCCccchhhHHHHHHhhhhcCCccccccc
Q 007785 119 CDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCM 164 (590)
Q Consensus 119 C~IC~e~~~~--~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP 164 (590)
|+||.+ +.. +.++.|+|||.||++|+...+.... ...++||
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 642 2367789999999999999988533 1358887
No 15
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=97.92 E-value=4.7e-06 Score=66.13 Aligned_cols=39 Identities=41% Similarity=1.045 Sum_probs=29.0
Q ss_pred CCcCCCC--CCcceeecCCCCe--eEec-cCceeeccccccccC
Q 007785 275 HTKPCPK--CHKPVEKNGGCNL--VSCI-CGQAFCWLCGGATGR 313 (590)
Q Consensus 275 ~tK~CPk--C~~~IEKn~GCNH--MtC~-Cg~~FCwlC~~~~~~ 313 (590)
+.+.||+ |...|++..|.++ |+|. |++.|||.|+++||.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 4589988 9999999999999 9996 999999999999743
No 16
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.77 E-value=1.9e-05 Score=60.05 Aligned_cols=46 Identities=26% Similarity=0.709 Sum_probs=36.3
Q ss_pred ccccccccccccccCceecCCCCc-cchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
...|.||++... +++.++|||. ||..|+..++.. ..+||. |+..+.
T Consensus 2 ~~~C~iC~~~~~--~~~~~pCgH~~~C~~C~~~~~~~--------~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--DVVLLPCGHLCFCEECAERLLKR--------KKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--SEEEETTCEEEEEHHHHHHHHHT--------TSBBTT--TTBB-S
T ss_pred cCCCccCCccCC--ceEEeCCCChHHHHHHhHHhccc--------CCCCCc--CChhhc
Confidence 468999999854 6778899999 999999999881 358998 887653
No 17
>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=97.70 E-value=3.2e-05 Score=56.14 Aligned_cols=43 Identities=33% Similarity=0.869 Sum_probs=32.9
Q ss_pred ccccccccccccCceec-CCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 118 MCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 118 ~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
+|+||++.+. .++.+ +|||.||..|+..|+.. + ..+||. |+..
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 5999999873 44444 69999999999999875 2 367987 7643
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.68 E-value=2.4e-05 Score=57.91 Aligned_cols=42 Identities=31% Similarity=0.886 Sum_probs=33.3
Q ss_pred ccccccccccc-cCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccc
Q 007785 118 MCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (590)
Q Consensus 118 ~C~IC~e~~~~-~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~ 169 (590)
.|+||++.+.. ..++.++|||.||..|+.... . ..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-----~---~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-----G---KSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-----C---CCCCCcC--CC
Confidence 49999999843 356667999999999999987 1 3579998 64
No 19
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=2.8e-05 Score=84.10 Aligned_cols=60 Identities=20% Similarity=0.503 Sum_probs=47.0
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhc
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 182 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 182 (590)
...||||++..+ -+..+.|||.||..|+-+||...... ....||. |...+....+..+..
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 678999999854 55667899999999999999987333 3479999 998887766554443
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=3.4e-05 Score=75.89 Aligned_cols=56 Identities=25% Similarity=0.548 Sum_probs=44.8
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (590)
...|+|.||+|.. .+++...|||.||-.|+-+|+....+. -.||. |+..++.+.+-
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vv 100 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVV 100 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEE
Confidence 5679999999984 488988999999999999999885432 46788 88777655443
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=97.48 E-value=9.2e-05 Score=58.62 Aligned_cols=47 Identities=9% Similarity=0.151 Sum_probs=38.4
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchH
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~ 175 (590)
+.|+||.+.+. +++.++|||.||+.|+..|+.. + ..||. |+..++..
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~~----~----~~cP~--~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLLS----H----GTDPV--TGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHHH----C----CCCCC--CcCCCChh
Confidence 67999999865 7888999999999999999975 1 37988 66666543
No 22
>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=97.46 E-value=8.3e-05 Score=51.94 Aligned_cols=38 Identities=34% Similarity=0.865 Sum_probs=30.5
Q ss_pred cccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 119 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 119 C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
|+||++. ...++.++|||.||..|+..|+. .+ ..+||.
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 34777889999999999999987 12 257875
No 23
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=9.3e-05 Score=75.47 Aligned_cols=44 Identities=30% Similarity=0.828 Sum_probs=37.6
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccc
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~ 169 (590)
.+.+.|+||++.+. .+..++|||.||..|+...+. ..+.||. |.
T Consensus 11 ~~~~~C~iC~~~~~--~p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFR--EPVLLPCGHNFCRACLTRSWE--------GPLSCPV--CR 54 (386)
T ss_pred cccccChhhHHHhh--cCccccccchHhHHHHHHhcC--------CCcCCcc--cC
Confidence 35689999999987 557779999999999999998 2389998 77
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=97.31 E-value=0.00013 Score=71.47 Aligned_cols=56 Identities=27% Similarity=0.538 Sum_probs=39.4
Q ss_pred cccccccccccccccc-----cC--ceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 113 LSSTVMCDICMEEVAG-----DK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~-----~~--~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
.+...+|+||++.+-. .. .+..+|+|.||..|+..|-..+...| ..-.||. |+..+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f 229 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRF 229 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Cccee
Confidence 3567899999998521 11 12339999999999999998653322 2357999 88654
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.30 E-value=0.00014 Score=78.14 Aligned_cols=66 Identities=24% Similarity=0.550 Sum_probs=47.0
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH-HHHhcCCCchHHHHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV-RNLVSKKHPNLAEKF 192 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i-~~ll~~~~~e~~eky 192 (590)
...+.|+||.+.+. .++.++|||.||..|+..|+.. . ..||. |...+....+ .+.+. .++++.|
T Consensus 24 e~~l~C~IC~d~~~--~PvitpCgH~FCs~CI~~~l~~-----~---~~CP~--Cr~~~~~~~Lr~N~~L---~~iVe~~ 88 (397)
T TIGR00599 24 DTSLRCHICKDFFD--VPVLTSCSHTFCSLCIRRCLSN-----Q---PKCPL--CRAEDQESKLRSNWLV---SEIVESF 88 (397)
T ss_pred ccccCCCcCchhhh--CccCCCCCCchhHHHHHHHHhC-----C---CCCCC--CCCccccccCccchHH---HHHHHHH
Confidence 45689999999875 6778899999999999999864 1 37998 8876654322 22222 3555666
Q ss_pred HH
Q 007785 193 ER 194 (590)
Q Consensus 193 ~~ 194 (590)
..
T Consensus 89 ~~ 90 (397)
T TIGR00599 89 KN 90 (397)
T ss_pred HH
Confidence 53
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=0.00011 Score=74.46 Aligned_cols=51 Identities=29% Similarity=0.665 Sum_probs=41.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i 177 (590)
....|.+|++... ++..++|||.||..|+..|...+- .||. |...+.+..+
T Consensus 238 a~~kC~LCLe~~~--~pSaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENRS--NPSATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCCC--CCCcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 4578999999844 888899999999999999988642 4998 9887766543
No 27
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.24 E-value=0.00019 Score=72.21 Aligned_cols=50 Identities=28% Similarity=0.569 Sum_probs=36.9
Q ss_pred ccccccccccccccccC------ceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 114 SSTVMCDICMEEVAGDK------ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~------~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
+...+|+||++.+...+ .+..+|+|.||..|+..|+.. ...||. |+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 34689999999865322 234589999999999998753 248999 886543
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.12 E-value=0.0003 Score=72.35 Aligned_cols=64 Identities=22% Similarity=0.543 Sum_probs=49.8
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHH-HhcCCCchHHHHHH
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRN-LVSKKHPNLAEKFE 193 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~-ll~~~~~e~~eky~ 193 (590)
...-|.||++-|. -++..+|+|.||.-|++.|+.. ...||. |...+.+..++. .+. .++++-|.
T Consensus 22 ~lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il---~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRIL---DEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHhc--CceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHH---HHHHHHHH
Confidence 4578999999976 5677799999999999999975 357998 998888777653 233 46666665
No 29
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=96.98 E-value=0.1 Score=56.15 Aligned_cols=120 Identities=19% Similarity=0.362 Sum_probs=72.3
Q ss_pred EeeCHHHHHHHHHHHHHHHHHHhCCCHH--HHHHHHHHcCCChHH--HHHHHHhcChhhhhHh---------hCCcccC-
Q 007785 40 KVITRESLLAAQKEDLRRVMELLSLREH--HARTLLIHYRWDVEK--LLAVLVENGKESLFNE---------AGVTVID- 105 (590)
Q Consensus 40 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~--~a~~LL~~~~W~~e~--l~~~~~~~~~~~~~~~---------~gl~~~~- 105 (590)
..+|.-||+.-+--.+..|.+|.-|..+ .-..+|+.|+=..+. .++.|..+....+-.+ +.+....
T Consensus 84 ~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Chll~V~~ve~~~s~d 163 (493)
T KOG0804|consen 84 AYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCHLLYVDRVEVTESED 163 (493)
T ss_pred ccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCccceeEEEEEEEEEEeccc
Confidence 3478999999999888888888766532 345677777765443 4444421111111111 0011000
Q ss_pred -CCCCCCCcccccccccccccccccC--ceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 106 -DADPMLPLSSTVMCDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 106 -~~~~~~~~~~~~~C~IC~e~~~~~~--~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
.+.++....+..+|+||++-.+.+- ..+..|.|.|.-.|+..|+. .+||. |+..
T Consensus 164 ~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~~ 220 (493)
T KOG0804|consen 164 GASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRYC 220 (493)
T ss_pred CCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhhh
Confidence 1111222346689999999876422 34568999999999998865 48988 6643
No 30
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.96 E-value=0.004 Score=66.00 Aligned_cols=35 Identities=17% Similarity=0.552 Sum_probs=29.6
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHh
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIV 151 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~ 151 (590)
+...|+||..-+. +++.|+|+|..|..|-..-+..
T Consensus 3 eelkc~vc~~f~~--epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYR--EPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhcc--CceEeecccHHHHHHHHhhccc
Confidence 4578999998776 8999999999999998876543
No 31
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.00065 Score=77.09 Aligned_cols=56 Identities=25% Similarity=0.650 Sum_probs=44.8
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNL 180 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~l 180 (590)
....+|++|..- ..+.+...|||.||..|++..+.++- =+||. |+..+...+|..+
T Consensus 641 K~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 356899999954 45788889999999999999998743 38998 8888887766543
No 32
>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=96.47 E-value=0.0015 Score=67.70 Aligned_cols=53 Identities=25% Similarity=0.510 Sum_probs=36.9
Q ss_pred cccccccccccc-cCceec--CCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHH
Q 007785 117 VMCDICMEEVAG-DKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (590)
Q Consensus 117 ~~C~IC~e~~~~-~~~~~l--~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (590)
..||||..+... ..+..+ +|||.||.+|+...|.. | +..||. |+..+....++
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 222112 79999999999999742 3 258996 98877655443
No 33
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.38 E-value=0.0023 Score=50.09 Aligned_cols=47 Identities=23% Similarity=0.508 Sum_probs=30.8
Q ss_pred cccccccccccccccCcee-cCCCCccchhhHHHHHHhhhhcCCcccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 169 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~ 169 (590)
..+.|||....+. +++. ..|||.|.++.+.+|+.. ...++||..||.
T Consensus 10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~------~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQR------NGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTT------TS-EE-SCCC-S
T ss_pred eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHh------cCCCCCCCCCCC
Confidence 4588999999865 6655 599999999999999921 245899999995
No 34
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.29 E-value=0.0023 Score=52.66 Aligned_cols=49 Identities=12% Similarity=0.101 Sum_probs=36.7
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
+.+.|+|+.+.+. +++.+++||.|++.|+..|+.. ....||. |+..+..
T Consensus 3 ~~f~CpIt~~lM~--dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMR--DPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-S--SEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SG
T ss_pred cccCCcCcCcHhh--CceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCc
Confidence 5699999999865 9999999999999999999986 1357888 5665554
No 35
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.01 E-value=0.0013 Score=52.21 Aligned_cols=43 Identities=23% Similarity=0.719 Sum_probs=21.8
Q ss_pred ccccccccccccccCceec-CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
...|++|.+.+. +++.| .|.|.||..|++..+. ..||. |..+-
T Consensus 7 lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPA 50 (65)
T ss_dssp TTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-
T ss_pred hcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC----------CCCCC--cCChH
Confidence 467999999865 78776 9999999999976432 25998 77654
No 36
>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=95.95 E-value=0.021 Score=41.97 Aligned_cols=40 Identities=23% Similarity=0.423 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhcC
Q 007785 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENG 91 (590)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~~~ 91 (590)
++.|...+++.|+++..|+.+|..++||++.-++.|++.+
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 3678899999999999999999999999999999999743
No 37
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.005 Score=62.81 Aligned_cols=52 Identities=21% Similarity=0.520 Sum_probs=41.6
Q ss_pred cccccccccccccccc-CceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 114 SSTVMCDICMEEVAGD-KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~-~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
....+|.||++.+... ....+||.|.|...|+..|+.. ...+||. |+..+++
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 3558999999998653 4566799999999999999874 3468998 9887764
No 38
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.76 E-value=0.0052 Score=61.78 Aligned_cols=53 Identities=30% Similarity=0.567 Sum_probs=40.5
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i 177 (590)
..+.|.||++.. ..+..++|||.||..|+-..|+.+ ..-.||. |++.+.+..|
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 368899999984 477888999999999999865542 1235998 8887665544
No 39
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.71 E-value=0.0073 Score=63.72 Aligned_cols=45 Identities=24% Similarity=0.485 Sum_probs=36.5
Q ss_pred ccccccccccccc-CceecCCCCccchhhHHHHHHhhhhcCCccccccccccc
Q 007785 117 VMCDICMEEVAGD-KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKC 168 (590)
Q Consensus 117 ~~C~IC~e~~~~~-~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C 168 (590)
.+|.||+|++... ....|+|.|.|...|+..||... + -.||.+++
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r----~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---R----TFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---C----ccCCCCCC
Confidence 7999999998764 45667999999999999999873 2 36999443
No 40
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.67 E-value=0.0053 Score=66.62 Aligned_cols=56 Identities=20% Similarity=0.475 Sum_probs=44.3
Q ss_pred cccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchH
Q 007785 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 175 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~ 175 (590)
+.....|.+|-++ ..+.+...|.|.||+-|+++|+....... .+.||. |...++.+
T Consensus 533 nk~~~~C~lc~d~--aed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 533 NKGEVECGLCHDP--AEDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred ccCceeecccCCh--hhhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 4467899999987 44778889999999999999998765443 389998 87665433
No 41
>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=95.53 E-value=0.0079 Score=49.50 Aligned_cols=41 Identities=24% Similarity=0.481 Sum_probs=29.1
Q ss_pred cccccccccccc----------cCce-ecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 117 VMCDICMEEVAG----------DKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 117 ~~C~IC~e~~~~----------~~~~-~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
..|.||++.+.. ..++ ...|||.|+..|+..++... -.||.
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 1223 34899999999999999652 28987
No 42
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.97 E-value=0.013 Score=59.48 Aligned_cols=47 Identities=28% Similarity=0.598 Sum_probs=37.4
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
...-|-||-+-+. -+...+|||.||.-|++.|+.+ ...||. |.....
T Consensus 24 s~lrC~IC~~~i~--ip~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRIS--IPCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPC 70 (391)
T ss_pred hHHHhhhhhheee--cceecccccchhHHHHHHHhcC--------CCCCcc--ccccHH
Confidence 4578999998866 5677799999999999999875 256888 776443
No 43
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.20 E-value=0.028 Score=45.86 Aligned_cols=56 Identities=25% Similarity=0.447 Sum_probs=26.0
Q ss_pred cccccccccccc-ccC-cee----cCCCCccchhhHHHHHHhhhhcCCcc-cc--cccccccccccc
Q 007785 116 TVMCDICMEEVA-GDK-ATK----MDCGHCFCNDCWTEHFIVKINEGQSK-RI--RCMAHKCNAICD 173 (590)
Q Consensus 116 ~~~C~IC~e~~~-~~~-~~~----l~CgH~FC~~C~~~yi~~~I~~g~~~-~i--~CP~~~C~~~~~ 173 (590)
...|+||+.... ... +.. ..|++.|...||.+||...-.....+ ++ .||. |...+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeee
Confidence 368999999754 222 221 26899999999999998765544322 22 6998 887664
No 44
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.026 Score=57.87 Aligned_cols=54 Identities=22% Similarity=0.492 Sum_probs=41.1
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 178 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~ 178 (590)
....+|.||+.+ ...++.|+|+|.||.-|++.-+.. +. ..|+. |...++...+.
T Consensus 5 ~~~~eC~IC~nt--~n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 5 TKKKECLICYNT--GNCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred ccCCcceeeecc--CCcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchhc
Confidence 345789999998 447799999999999999875432 22 46988 99888766543
No 45
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.65 E-value=0.13 Score=52.15 Aligned_cols=51 Identities=22% Similarity=0.540 Sum_probs=37.9
Q ss_pred cccccccccccccccccCceec-CCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 113 LSSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
.+...+|++|-+.- ..|..+ +|||.||--|+..-+... ..++||. |+..+.
T Consensus 236 ~t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 34568999998873 345555 699999999998876542 2479998 887654
No 46
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.39 E-value=0.25 Score=52.88 Aligned_cols=39 Identities=36% Similarity=0.765 Sum_probs=34.9
Q ss_pred hCCcCCCC--CCcceeecCCCCeeEe-ccCceeecccccccc
Q 007785 274 VHTKPCPK--CHKPVEKNGGCNLVSC-ICGQAFCWLCGGATG 312 (590)
Q Consensus 274 ~~tK~CPk--C~~~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~ 312 (590)
.+..-||+ |..|+-...|++-..| +|.+.||.+|...||
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H 312 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH 312 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc
Confidence 45789999 9999977889999999 799999999998863
No 47
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=93.24 E-value=0.056 Score=56.75 Aligned_cols=48 Identities=27% Similarity=0.630 Sum_probs=37.2
Q ss_pred ccccccccccc-cccc----------CceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 115 STVMCDICMEE-VAGD----------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 115 ~~~~C~IC~e~-~~~~----------~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
....|.||+|+ +... .+..++|||.+...|++.|++.+ -.||. |+.++
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 24678999999999999998752 38998 87653
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.89 E-value=0.064 Score=40.36 Aligned_cols=44 Identities=30% Similarity=0.708 Sum_probs=21.5
Q ss_pred ccccccccccc--CceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 119 CDICMEEVAGD--KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 119 C~IC~e~~~~~--~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
|++|.++++.. ++...+||+.+|..||..-+.. .+ =+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~~----g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---EG----GRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S-----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---cC----CCCCC--CCCC
Confidence 78999987543 3344589999999999887652 12 37987 7754
No 49
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.78 E-value=0.046 Score=59.23 Aligned_cols=41 Identities=32% Similarity=0.754 Sum_probs=32.8
Q ss_pred cccccCCCCCCCCceEeecCcccceeeccCCCeeecCccCcCCCC
Q 007785 205 KMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSP 249 (590)
Q Consensus 205 ~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p 249 (590)
...+-|| .|...|..... ...++|.||+.||+.|+.+|+..
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 79988875544 66799999999999999888653
No 50
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.59 E-value=0.14 Score=55.58 Aligned_cols=49 Identities=24% Similarity=0.595 Sum_probs=37.5
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
...+.|.||+..+. ++++++|||.||..|+..-+. ..-.||. |...+..
T Consensus 82 ~sef~c~vc~~~l~--~pv~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY--PPVVTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC--CCccccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 46799999998866 788889999999999766322 1247887 8876653
No 51
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.37 E-value=0.027 Score=58.90 Aligned_cols=47 Identities=30% Similarity=0.669 Sum_probs=35.0
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
..+.|+||++-+.. -+....|+|+||.+|+-.-+.. |. -.||. |+..
T Consensus 42 ~~v~c~icl~llk~-tmttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~ 88 (381)
T KOG0311|consen 42 IQVICPICLSLLKK-TMTTKECLHRFCFDCIWKALRS----GN---NECPT--CRKK 88 (381)
T ss_pred hhhccHHHHHHHHh-hcccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhh
Confidence 56899999998652 4556699999999998766543 32 37988 7654
No 52
>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=92.14 E-value=0.067 Score=35.02 Aligned_cols=23 Identities=39% Similarity=0.953 Sum_probs=16.5
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCcee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~F 303 (590)
|.||.|+..|-.+. ..|. |||.|
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 67999998886433 5674 88776
No 53
>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=92.05 E-value=5.7 Score=41.69 Aligned_cols=53 Identities=28% Similarity=0.670 Sum_probs=34.6
Q ss_pred cCCCCCCCCceEeecCcccceeeccCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCcceee
Q 007785 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEK 288 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEK 288 (590)
-|| .|..-....+.....+. +|||.||..|.... | .....+||.|+.++.|
T Consensus 5 ~CP---~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----------~--------------~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCP---RCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----------F--------------VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCC---cCCCCCccCcccccccC-CCCCcccHHHHHHH-----------h--------------cCCCCCCCCCCCccch
Confidence 487 68765554444333455 79999999997531 1 1123589999999886
Q ss_pred cC
Q 007785 289 NG 290 (590)
Q Consensus 289 n~ 290 (590)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 53
No 54
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.94 E-value=0.05 Score=52.40 Aligned_cols=32 Identities=28% Similarity=0.816 Sum_probs=27.2
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHH
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEH 148 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~y 148 (590)
-.|.|.||-.++. .++...|||.||..|...-
T Consensus 195 IPF~C~iCKkdy~--spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 195 IPFLCGICKKDYE--SPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred Cceeehhchhhcc--chhhhhcchhHHHHHHHHH
Confidence 3589999999987 7888899999999997553
No 55
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.66 E-value=0.11 Score=55.04 Aligned_cols=56 Identities=25% Similarity=0.469 Sum_probs=37.6
Q ss_pred cccccccccccccccccC-----cee-cCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 113 LSSTVMCDICMEEVAGDK-----ATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
.+...+|.||++.+.... .-. .+|.|.||..|++.|=...-. +....-.||. |+..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~ 219 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVP 219 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCc
Confidence 356789999999865322 222 379999999999998643222 2213457998 7753
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.45 E-value=0.5 Score=48.83 Aligned_cols=148 Identities=20% Similarity=0.362 Sum_probs=75.8
Q ss_pred HHHHcCCChHHHHHHHHhcChhhhhHhh-CCcccCCCCCCCCcccccccccccccccccCceec--CCCCccchhhHHHH
Q 007785 72 LLIHYRWDVEKLLAVLVENGKESLFNEA-GVTVIDDADPMLPLSSTVMCDICMEEVAGDKATKM--DCGHCFCNDCWTEH 148 (590)
Q Consensus 72 LL~~~~W~~e~l~~~~~~~~~~~~~~~~-gl~~~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l--~CgH~FC~~C~~~y 148 (590)
-|.||+-=.+.-++.|-..+.++..... |+.-+.+. |..=+-.-+...-++. .||-.||+.|+..|
T Consensus 286 e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pg-----------CG~gll~EPD~rkvtC~~gCgf~FCR~C~e~y 354 (446)
T KOG0006|consen 286 ELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPG-----------CGAGLLPEPDQRKVTCEGGCGFAFCRECKEAY 354 (446)
T ss_pred hhhhheecchhHHHHHHHhhhhhheeecCCEecCCCC-----------CCcccccCCCCCcccCCCCchhHhHHHHHhhh
Confidence 3557777777777777665555544433 43322211 1111111011111222 59999999999998
Q ss_pred HHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHHHHHHhhhhhhcCcccccCCCCCCCCceEeecCcccc
Q 007785 149 FIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVC 228 (590)
Q Consensus 149 i~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~ 228 (590)
-...-..+.... -...|...+++... ...+|+...-. ......+.|| .|..+.... ....
T Consensus 355 h~geC~~~~~as---~t~tc~y~vde~~a----------~~arwd~as~~---TIk~tTkpCP---kChvptErn-GGCm 414 (446)
T KOG0006|consen 355 HEGECSAVFEAS---GTTTCAYRVDERAA----------EQARWDAASKE---TIKKTTKPCP---KCHVPTERN-GGCM 414 (446)
T ss_pred ccccceeeeccc---cccceeeecChhhh----------hhhhhhhhhhh---hhhhccCCCC---CccCccccC-CceE
Confidence 543222111000 01124433433221 12334333221 1123457788 787666543 3445
Q ss_pred eeec--c-CCCeeecCccCcCCCCC
Q 007785 229 EVEC--A-CGAQFCFSCLSEAHSPC 250 (590)
Q Consensus 229 ~v~C--~-Cg~~fC~~C~~~~H~p~ 250 (590)
.+.| + ||..+||.|+.+|...+
T Consensus 415 Hm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 415 HMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred EeecCCCCCCceeEeccCChhhhhh
Confidence 6789 3 99999999999987643
No 57
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.30 E-value=0.11 Score=53.92 Aligned_cols=46 Identities=24% Similarity=0.643 Sum_probs=35.4
Q ss_pred cccccccccccccccCcee-cCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
...+|.+|-.-+- +..+ ..|-|.||++||-.|+.. .-.||. |...+
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 4589999987754 4444 489999999999999987 148998 66544
No 58
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=90.90 E-value=0.5 Score=49.22 Aligned_cols=48 Identities=21% Similarity=0.481 Sum_probs=36.2
Q ss_pred cccccccccccccccCceec-CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
....|+||+.... ++..+ --|-.||-.|+..|+.. .| +||..+|+..+
T Consensus 299 ~~~~CpvClk~r~--Nptvl~vSGyVfCY~Ci~~Yv~~---~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ--NPTVLEVSGYVFCYPCIFSYVVN---YG-----HCPVTGYPASV 347 (357)
T ss_pred ccccChhHHhccC--CCceEEecceEEeHHHHHHHHHh---cC-----CCCccCCcchH
Confidence 4578999998743 44444 56999999999999983 33 69998887654
No 59
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.79 E-value=0.29 Score=51.02 Aligned_cols=55 Identities=27% Similarity=0.666 Sum_probs=40.9
Q ss_pred ccccccccccccc----CceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccc--cchHHHHHH
Q 007785 117 VMCDICMEEVAGD----KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI--CDEAVVRNL 180 (590)
Q Consensus 117 ~~C~IC~e~~~~~----~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~--~~~~~i~~l 180 (590)
..|.||-++++.. -|..|.|||.+|..|....+.. ..+.||. |... ++...++.+
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 2556789999999999988764 3478877 8876 444455443
No 60
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=90.39 E-value=0.38 Score=58.10 Aligned_cols=66 Identities=24% Similarity=0.506 Sum_probs=52.5
Q ss_pred ccccccccccc-ccccCceecCCCCccchhhHHHHHHhhhhcCC--cccccccccccccccchHHHHHHhc
Q 007785 115 STVMCDICMEE-VAGDKATKMDCGHCFCNDCWTEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVS 182 (590)
Q Consensus 115 ~~~~C~IC~e~-~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~ 182 (590)
..-.|.|||.+ +.....+.|.|+|.|...|-+.-+...-.... +.-|.||. |...+....++.++.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLld 3553 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLD 3553 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHH
Confidence 45679999988 45556778999999999999998887665433 24579999 999998888888875
No 61
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.26 E-value=1.2 Score=47.71 Aligned_cols=126 Identities=15% Similarity=0.214 Sum_probs=70.4
Q ss_pred EeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhcChhhhhHh-hCCcccCCC-------CCCC
Q 007785 40 KVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNE-AGVTVIDDA-------DPML 111 (590)
Q Consensus 40 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~~~~~~~~~~-~gl~~~~~~-------~~~~ 111 (590)
..|++.......++-+++-..+||++.....-++...+-..=-.+-.+. .++.. .|.-..... ....
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 3455566666666777788888888876655555444333222222221 11111 111100000 0001
Q ss_pred Ccccccccccccccccc-cCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH
Q 007785 112 PLSSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (590)
Q Consensus 112 ~~~~~~~C~IC~e~~~~-~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i 177 (590)
..-+.|.|||=-+..+. +.|..|.|||..|++=+..... +|. ..++||- |+........
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 12256899998776543 5677889999999988777644 343 4689998 8865544443
No 62
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.03 E-value=0.15 Score=57.88 Aligned_cols=45 Identities=27% Similarity=0.701 Sum_probs=35.7
Q ss_pred cccccccccccccc---CceecCCCCccchhhHHHHHHhhhhcCCccccccccccc
Q 007785 116 TVMCDICMEEVAGD---KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKC 168 (590)
Q Consensus 116 ~~~C~IC~e~~~~~---~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C 168 (590)
...|.||.+..... .+..++|+|.||..|++.|+.. .-.||.+.+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~CR~ 338 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPTCRT 338 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCcchh
Confidence 57899999996521 1577899999999999999987 147998333
No 63
>PRK00420 hypothetical protein; Validated
Probab=89.59 E-value=2.9 Score=37.39 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=20.6
Q ss_pred CcCCCCCCcceeecCCCCeeEeccCceeecccccc
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 310 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~ 310 (590)
...||.|+.|+.+. +-|..||-.|+..
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 48999999998751 2347888888876
No 64
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.16 E-value=0.25 Score=52.66 Aligned_cols=49 Identities=22% Similarity=0.672 Sum_probs=37.5
Q ss_pred ccccccccccccc---cCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 116 TVMCDICMEEVAG---DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 116 ~~~C~IC~e~~~~---~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
..+|+||++.+.. ..++++.|||-|=.+|+..|+. ++ ...+||. |...-
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 4689999998543 3467889999999999999993 22 3468998 66543
No 65
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.43 E-value=0.27 Score=51.40 Aligned_cols=52 Identities=31% Similarity=0.616 Sum_probs=37.9
Q ss_pred CCcccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 111 LPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 111 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
.|.++...|+||+-. +-..+..+|+|.-|.+|+.+++-.. -+|.. |+..+..
T Consensus 417 lp~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN~--------k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMNC--------KRCFF--CKTTVID 468 (489)
T ss_pred CCCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhcC--------CeeeE--ecceeee
Confidence 455677899999976 2234556999999999999997641 36766 7776543
No 66
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=87.80 E-value=0.42 Score=40.43 Aligned_cols=31 Identities=19% Similarity=0.498 Sum_probs=24.8
Q ss_pred CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 135 DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 135 ~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
.|+|.|..-|+.+++.++-. .-.||. |+...
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w 81 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPW 81 (85)
T ss_pred cCccHHHHHHHHHHHccccC-----CCCCCC--cCCee
Confidence 79999999999999997522 237998 87654
No 67
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=86.64 E-value=0.29 Score=51.91 Aligned_cols=47 Identities=30% Similarity=0.720 Sum_probs=34.9
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
-.-|.||-+. ..++..-+|||..|..|+..|=.. .+|+ .||.+.|..
T Consensus 369 FeLCKICaen--dKdvkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcEI 415 (563)
T KOG1785|consen 369 FELCKICAEN--DKDVKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCEI 415 (563)
T ss_pred HHHHHHhhcc--CCCcccccccchHHHHHHHhhccc--CCCC----CCCceeeEe
Confidence 3469999986 335666699999999999998543 2355 899966653
No 68
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=86.19 E-value=0.54 Score=35.57 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=31.4
Q ss_pred ccccccccccccCceecCCC-----CccchhhHHHHHHhhhhcCCcccccccc
Q 007785 118 MCDICMEEVAGDKATKMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~Cg-----H~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
.|-||++.....++...||. |.+...|+..|+..+-+ .+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~------~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGN------KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCC------CcCCC
Confidence 48899984444566677885 88999999999987432 47876
No 69
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=86.18 E-value=0.19 Score=49.97 Aligned_cols=49 Identities=22% Similarity=0.545 Sum_probs=36.2
Q ss_pred cccccccccccc-cCceec---CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 117 VMCDICMEEVAG-DKATKM---DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 117 ~~C~IC~e~~~~-~~~~~l---~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
-.||||-.+.-. -++..+ .|-|..|-+|.-..|+. | +-.||.++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G---pAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G---PAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C---CCCCCCccHHHHH
Confidence 479999888322 233333 49999999999988764 3 4789999998654
No 70
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.08 E-value=0.65 Score=49.00 Aligned_cols=48 Identities=23% Similarity=0.538 Sum_probs=36.6
Q ss_pred ccccccccccccccccCceecCCCCc-cchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~-FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
....+|.||+.+. .+.+.|+|.|. .|.+|-+..- ... =.||. |+..+.
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 4468999999984 48899999996 8999987664 111 26999 887653
No 71
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.93 E-value=0.41 Score=48.51 Aligned_cols=52 Identities=27% Similarity=0.620 Sum_probs=39.8
Q ss_pred ccccccccccccccc--------CceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 115 STVMCDICMEEVAGD--------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~--------~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
+...|.||-..+..+ +...|+|+|.|...|++.+... |+ .-.||- |+..++.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK--kqtCPY--CKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK--KQTCPY--CKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC--CCCCch--HHHHhhH
Confidence 456899998875432 5678999999999999999765 22 358998 8877653
No 72
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.40 E-value=0.45 Score=51.89 Aligned_cols=52 Identities=21% Similarity=0.417 Sum_probs=37.0
Q ss_pred ccccccccccccccccc-----Cc----------eecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 113 LSSTVMCDICMEEVAGD-----KA----------TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~-----~~----------~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
......|.||+.+++.. .+ ...+|.|.|...|+.+++.+ ..+.||. |+.+++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCC
Confidence 34567899999987631 11 12399999999999999875 2368998 555443
No 73
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=84.66 E-value=0.39 Score=44.03 Aligned_cols=34 Identities=32% Similarity=0.703 Sum_probs=27.7
Q ss_pred ccccccccccccc-cCceecCCC------CccchhhHHHHH
Q 007785 116 TVMCDICMEEVAG-DKATKMDCG------HCFCNDCWTEHF 149 (590)
Q Consensus 116 ~~~C~IC~e~~~~-~~~~~l~Cg------H~FC~~C~~~yi 149 (590)
..+|.||++.+.. +-++.++|| |.||.+|++.|=
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 5799999999875 345666777 889999999983
No 74
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=83.71 E-value=2.8 Score=43.29 Aligned_cols=37 Identities=22% Similarity=0.385 Sum_probs=30.2
Q ss_pred cccccccccccccC-ceecCCCCccchhhHHHHHHhhh
Q 007785 117 VMCDICMEEVAGDK-ATKMDCGHCFCNDCWTEHFIVKI 153 (590)
Q Consensus 117 ~~C~IC~e~~~~~~-~~~l~CgH~FC~~C~~~yi~~~I 153 (590)
..|.||+--|...+ +...+|.|+|..-|+..|+....
T Consensus 116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 67888888776655 55669999999999999998743
No 75
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.62 E-value=0.53 Score=29.87 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=8.7
Q ss_pred CCCCCCcceeec
Q 007785 278 PCPKCHKPVEKN 289 (590)
Q Consensus 278 ~CPkC~~~IEKn 289 (590)
.||+|+..|+.+
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 388888888743
No 76
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=82.75 E-value=0.71 Score=49.67 Aligned_cols=69 Identities=17% Similarity=0.207 Sum_probs=32.2
Q ss_pred cccceeec-cCCCe----eecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee-e--cCCC----
Q 007785 225 VEVCEVEC-ACGAQ----FCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE-K--NGGC---- 292 (590)
Q Consensus 225 ~~~~~v~C-~Cg~~----fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE-K--n~GC---- 292 (590)
+....|.| .|-+. -|..|..+.-..--+++.-+.+...+ -...+.-.|--|+..+- + ..||
T Consensus 378 d~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr-------~fHv~CY~CEDCg~~LS~e~e~qgCyPld 450 (468)
T KOG1701|consen 378 DSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDR-------DFHVNCYKCEDCGLLLSSEEEGQGCYPLD 450 (468)
T ss_pred cCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccc-------cccccceehhhcCccccccCCCCcceecc
Confidence 44456777 35443 47777766543333322111110000 01223346667777765 3 3455
Q ss_pred CeeEec-cC
Q 007785 293 NLVSCI-CG 300 (590)
Q Consensus 293 NHMtC~-Cg 300 (590)
||+.|+ |+
T Consensus 451 ~HllCk~Ch 459 (468)
T KOG1701|consen 451 GHLLCKTCH 459 (468)
T ss_pred Cceeechhh
Confidence 566663 54
No 77
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.51 E-value=0.83 Score=52.42 Aligned_cols=18 Identities=11% Similarity=0.018 Sum_probs=10.6
Q ss_pred CCCccchhhHHHHHHhhh
Q 007785 136 CGHCFCNDCWTEHFIVKI 153 (590)
Q Consensus 136 CgH~FC~~C~~~yi~~~I 153 (590)
|+|.+|..||..+...-+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhHHHHHHHHHhh
Confidence 666666666666655444
No 78
>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=82.05 E-value=4.6 Score=28.35 Aligned_cols=34 Identities=24% Similarity=0.382 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHH
Q 007785 52 KEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAV 86 (590)
Q Consensus 52 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~ 86 (590)
.+.|.+++++ |.+...|+.-|+..+||++..++.
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 3567888888 999999999999999999987654
No 79
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=81.63 E-value=0.55 Score=54.46 Aligned_cols=47 Identities=30% Similarity=0.660 Sum_probs=36.0
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
+.|.||.+ ...++...|+|.||.+||..+|...-. -.||. |...+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC------CCCcH--HHHHHHH
Confidence 89999999 346778899999999999999876322 26766 7765443
No 80
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=81.16 E-value=1.3 Score=33.37 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=19.8
Q ss_pred cCCCCCCcceeecC--CCCeeEec-cCcee
Q 007785 277 KPCPKCHKPVEKNG--GCNLVSCI-CGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~--GCNHMtC~-Cg~~F 303 (590)
+.||.|+.++.... +-+++.|+ ||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46999998887543 35689994 99764
No 81
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=81.13 E-value=0.4 Score=48.00 Aligned_cols=45 Identities=24% Similarity=0.549 Sum_probs=32.2
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
+.|..|+---+....+.+.|+|.||..|.+.- .+-.||. |+..+.
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 57998987655445555699999999997542 1227988 887653
No 82
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=80.19 E-value=4 Score=36.98 Aligned_cols=110 Identities=15% Similarity=0.233 Sum_probs=51.6
Q ss_pred cchHHHHHHhcC-CCchHHHHHHHHHhhhhhhcCcccccCCCCCCCCceEeecCcccceeeccCCCeeecCccCcC--CC
Q 007785 172 CDEAVVRNLVSK-KHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEA--HS 248 (590)
Q Consensus 172 ~~~~~i~~ll~~-~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~--H~ 248 (590)
++-...+++++. ++.+-+.+|...+-...--+.+-+ =| -=...+...+.....+.|.||++||-- ...| |.
T Consensus 17 l~w~qt~r~msa~kdhdrf~kylavlqdrv~~~dpil--lp---vg~hlfi~qs~~~rv~rcecghsf~d~-r~nwkl~a 90 (165)
T COG4647 17 LPWPQTRRMMSAYKDHDRFFKYLAVLQDRVDWDDPIL--LP---VGDHLFICQSAQKRVIRCECGHSFGDY-RENWKLHA 90 (165)
T ss_pred CCcHHHHHHHhccccHHHHHHHHHHHHhhcccCCCee--ee---cCCcEEEEecccccEEEEeccccccCh-hhCceeee
Confidence 444556666662 334555555544433211111111 12 112233333333345789999999975 3334 22
Q ss_pred CCCchhh-HHHHHhh-hchHHhHHHHHhCCcCCCCCCccee
Q 007785 249 PCSCSMW-DLWAKKC-RDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 249 p~sC~~~-~~w~~~~-~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
...-... .+..+.. ..+...-+|+...--.||.|+...+
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 2111100 0111000 1122234677666678999999887
No 83
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.63 E-value=1.1 Score=44.71 Aligned_cols=42 Identities=31% Similarity=0.767 Sum_probs=27.2
Q ss_pred ecCcccceeeccCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee
Q 007785 222 VEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 222 ~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
.+....+.|+| |||.|||-|.. +|.. +..+.+.||-|+..|.
T Consensus 54 Ld~akdPVvTl-CGHLFCWpCly------------qWl~-----------~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 54 LDLAKDPVVTL-CGHLFCWPCLY------------QWLQ-----------TRPNSKECPVCKAEVS 95 (230)
T ss_pred ccccCCCEEee-cccceehHHHH------------HHHh-----------hcCCCeeCCccccccc
Confidence 33333344555 99999999975 3432 1234588999988776
No 84
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.52 E-value=1.1 Score=49.72 Aligned_cols=37 Identities=35% Similarity=0.755 Sum_probs=31.5
Q ss_pred CcCCC--CCCcceee-cCCCCeeEeccCceeecccccccc
Q 007785 276 TKPCP--KCHKPVEK-NGGCNLVSCICGQAFCWLCGGATG 312 (590)
Q Consensus 276 tK~CP--kC~~~IEK-n~GCNHMtC~Cg~~FCwlC~~~~~ 312 (590)
.|-|| .|+..+.- .+.+.-+.|.|++.|||.|+.+||
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH 197 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence 46676 59888887 788999999999999999998864
No 85
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.94 E-value=0.76 Score=47.29 Aligned_cols=45 Identities=27% Similarity=0.691 Sum_probs=34.4
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
.|-|.||-..+- .++...|+|.||..|....+.. | -+|+. |....
T Consensus 241 Pf~c~icr~~f~--~pVvt~c~h~fc~~ca~~~~qk----~----~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVVTKCGHYFCEVCALKPYQK----G----EKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccc--cchhhcCCceeehhhhcccccc----C----Cccee--ccccc
Confidence 477999999976 7888899999999997665542 2 36776 76543
No 86
>PHA00626 hypothetical protein
Probab=78.56 E-value=1.6 Score=33.82 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=21.3
Q ss_pred CCCCCCc-ceeecCCCCe----eEe-ccCceeecc
Q 007785 278 PCPKCHK-PVEKNGGCNL----VSC-ICGQAFCWL 306 (590)
Q Consensus 278 ~CPkC~~-~IEKn~GCNH----MtC-~Cg~~FCwl 306 (590)
.||+|+. -|-|++-|+. ..| .||+.|=-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 6999998 5878777654 678 488877543
No 87
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.10 E-value=1.3 Score=51.09 Aligned_cols=25 Identities=48% Similarity=1.034 Sum_probs=16.9
Q ss_pred cCCCCCCcceeecCCCCeeEeccCceeecccccccc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~~ 312 (590)
+.||+|+..+.. +..||..||.+.+
T Consensus 28 ~~Cp~CG~~~~~-----------~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTEVPV-----------DEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCCCCc-----------ccccccccCCccc
Confidence 567777777653 3458888887644
No 88
>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=77.85 E-value=8 Score=27.97 Aligned_cols=38 Identities=24% Similarity=0.344 Sum_probs=33.1
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 007785 52 KEDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (590)
Q Consensus 52 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~e~l~~~~~~ 89 (590)
.+.|..+++++ +++....+..|..++++++..++.+.+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 35788999999 799999999999999999999998874
No 89
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=77.11 E-value=1.5 Score=47.83 Aligned_cols=47 Identities=30% Similarity=0.795 Sum_probs=36.3
Q ss_pred cccccccccccccccccCcee-cCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 113 LSSTVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
......|++|...+. +++. ..|||.||..|+..+... ...||. |...
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~ 65 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQE 65 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc--------CcCCcc--cccc
Confidence 456789999999866 6666 599999999999998775 246776 5443
No 90
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.63 E-value=1.3 Score=28.89 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=9.1
Q ss_pred cCCCCCCcceee
Q 007785 277 KPCPKCHKPVEK 288 (590)
Q Consensus 277 K~CPkC~~~IEK 288 (590)
+.||+|+..|..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 678888887664
No 91
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.58 E-value=0.76 Score=35.38 Aligned_cols=45 Identities=27% Similarity=0.475 Sum_probs=32.4
Q ss_pred cccccccccccccCceecCCCCc-cchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~-FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
-+|.||++.- -+.+.-.|||. .|.+|-...+.. .. -.||. |+.++
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~--~~-----g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA--LH-----GCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc--cC-----CcCcc--hhhHH
Confidence 6899999972 24445589997 899998887765 12 36887 77654
No 92
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=75.09 E-value=1.9 Score=31.74 Aligned_cols=30 Identities=33% Similarity=0.604 Sum_probs=23.0
Q ss_pred HHHHhCCcCCCCCCcceeecCCCCeeEec---cCcee
Q 007785 270 NWITVHTKPCPKCHKPVEKNGGCNLVSCI---CGQAF 303 (590)
Q Consensus 270 ~~i~~~tK~CPkC~~~IEKn~GCNHMtC~---Cg~~F 303 (590)
.|.....+.||+|++.- |+--+.|+ |++.|
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 46677889999999876 77778883 77655
No 93
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.97 E-value=1.1 Score=47.76 Aligned_cols=48 Identities=27% Similarity=0.652 Sum_probs=33.7
Q ss_pred cccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 116 TVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 116 ~~~C~IC~e~~~~~-~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
...|.||-+-++.. +...+ .|||.|...|+.+|+...-.. -.||. |..
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~i 53 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQI 53 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eee
Confidence 35799996655542 34445 599999999999999864332 25887 553
No 94
>PF04641 Rtf2: Rtf2 RING-finger
Probab=74.12 E-value=2.3 Score=43.62 Aligned_cols=58 Identities=21% Similarity=0.434 Sum_probs=42.3
Q ss_pred cccccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhc
Q 007785 114 SSTVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 182 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~-~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 182 (590)
...+.|||...++... .++.+ +|||.|+..++++. ..+ -.||. |...+...+|-.|.+
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 4679999999998643 34455 99999999999987 111 25998 998887665544444
No 95
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=73.59 E-value=0.52 Score=48.31 Aligned_cols=35 Identities=31% Similarity=0.623 Sum_probs=26.2
Q ss_pred HHhCCcCCCCCCcceeecCCCCeeEe-ccCceeecccccccc
Q 007785 272 ITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATG 312 (590)
Q Consensus 272 i~~~tK~CPkC~~~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~ 312 (590)
+..++.+|--|-...+ |-+| .|||-|||-|...|-
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 3445677777766665 4678 599999999998864
No 96
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=72.78 E-value=2 Score=32.71 Aligned_cols=29 Identities=24% Similarity=0.520 Sum_probs=20.3
Q ss_pred hCCcCCCCCCc-ceeecCCCCeeEe-ccCceee
Q 007785 274 VHTKPCPKCHK-PVEKNGGCNLVSC-ICGQAFC 304 (590)
Q Consensus 274 ~~tK~CPkC~~-~IEKn~GCNHMtC-~Cg~~FC 304 (590)
..-+.||+|+. .+.... +.+.| +||+.+-
T Consensus 18 ~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHL--DRWHCGKCGYTEF 48 (50)
T ss_pred EccCcCcCCCcchheccC--CcEECCCcCCEEe
Confidence 34579999988 443333 67999 6998753
No 97
>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=72.47 E-value=3.8 Score=42.21 Aligned_cols=48 Identities=27% Similarity=0.701 Sum_probs=33.4
Q ss_pred cccccccccc-ccCceec--CCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 118 MCDICMEEVA-GDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 118 ~C~IC~e~~~-~~~~~~l--~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
.|++|-.+.- .-+++.+ +|+|..|.+|+-..+.. | +-.|| .|..++..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g---~~~Cp--eC~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G---PAQCP--ECMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C---CCCCC--cccchhhh
Confidence 4899987732 2233333 99999999999888764 2 35798 49876643
No 98
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.78 E-value=2.5 Score=43.49 Aligned_cols=28 Identities=32% Similarity=0.911 Sum_probs=22.9
Q ss_pred ccccccccccccccCceecCCCCc-cchhhH
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHC-FCNDCW 145 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~-FC~~C~ 145 (590)
...|.||++. +.+.+.|+|||. -|..|=
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhc
Confidence 5789999998 348899999996 688773
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=70.41 E-value=1.8 Score=37.50 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=26.0
Q ss_pred cccccccccccccccCceecCCCCccchhhHH
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWT 146 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~ 146 (590)
+...|++|...+..+.++..||||.|+..|.+
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 34679999999876666667999999999975
No 100
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.95 E-value=2.5 Score=42.47 Aligned_cols=53 Identities=8% Similarity=0.221 Sum_probs=38.2
Q ss_pred ccccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH
Q 007785 115 STVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~-~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i 177 (590)
..+.|+||-+.++.. ....| +|||.||..|...+|.. ...||. |...+.+..|
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 568899999997632 23334 99999999999998764 245776 6666655544
No 101
>PLN03086 PRLI-interacting factor K; Provisional
Probab=69.46 E-value=9.6 Score=43.35 Aligned_cols=57 Identities=26% Similarity=0.570 Sum_probs=33.5
Q ss_pred ccccccccccccccchHHHHHHhcCCCchHHHHHHHHHhhhhhhcCcccccCCCCCCCCceEeecCcccceeecc-CCCe
Q 007785 159 KRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (590)
Q Consensus 159 ~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (590)
..+.||. |...++...+...+. .-..+.+-|| ..+|+..+....-.. ...|+ |+..
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 3468988 888776655543322 1122345688 357999887554322 24675 7666
Q ss_pred e
Q 007785 238 F 238 (590)
Q Consensus 238 f 238 (590)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 5
No 102
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=69.46 E-value=3.9 Score=29.34 Aligned_cols=33 Identities=21% Similarity=0.627 Sum_probs=26.4
Q ss_pred cCCCCCCcc-eeecCCCCeeEe-ccCceeeccccccccCCCc
Q 007785 277 KPCPKCHKP-VEKNGGCNLVSC-ICGQAFCWLCGGATGRDHT 316 (590)
Q Consensus 277 K~CPkC~~~-IEKn~GCNHMtC-~Cg~~FCwlC~~~~~~~H~ 316 (590)
..|+.|... +. ++| .|+..+|..|....+.+|.
T Consensus 4 ~~C~~H~~~~~~-------~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp SB-SSTTTSBEE-------EEETTTTEEEEHHHHHTSTTTSE
T ss_pred ccCccCCccceE-------EEecCCCCccCccCCCCCCCCCE
Confidence 689999987 77 999 5999999999987555553
No 103
>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=69.16 E-value=6.2 Score=26.88 Aligned_cols=28 Identities=25% Similarity=0.655 Sum_probs=16.4
Q ss_pred CCcCCCCCCcceeecCCCCeeEe-ccCce
Q 007785 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (590)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCNHMtC-~Cg~~ 302 (590)
+.+-||+|+.+.....+=--|.| .|++.
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 34788888888888777666888 48765
No 104
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=68.65 E-value=2.5 Score=30.83 Aligned_cols=28 Identities=36% Similarity=0.799 Sum_probs=19.6
Q ss_pred CCCCCcceeecCCCCeeEeccCceeeccccccc
Q 007785 279 CPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (590)
Q Consensus 279 CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~ 311 (590)
||-|...+. +-++=.|||.||..|+..+
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~ 28 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERL 28 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHH
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHH
Confidence 566666665 3356679999999999875
No 105
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=68.36 E-value=2 Score=44.89 Aligned_cols=52 Identities=23% Similarity=0.522 Sum_probs=37.2
Q ss_pred ccccccccccccc--cCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHH
Q 007785 116 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 176 (590)
Q Consensus 116 ~~~C~IC~e~~~~--~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~ 176 (590)
.-.|+.|.++.+. .+++..+||-..|.-||... ...+ .=+||. |+...+++-
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~l------ngrcpa--crr~y~den 67 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNL------NGRCPA--CRRKYDDEN 67 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhc------cCCChH--hhhhccccc
Confidence 3459999998654 45777899999999999764 3222 238998 886555443
No 106
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=67.80 E-value=3.6 Score=48.06 Aligned_cols=50 Identities=26% Similarity=0.440 Sum_probs=38.8
Q ss_pred ccccccccccccccc-Cceec-CCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 115 STVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~-~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
..++|.||++.+... .+.+. .|-|.|...|++.|....-.+|. ...+||.
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 468999999997653 44555 78999999999999988555544 4578887
No 107
>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=67.32 E-value=20 Score=25.99 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=33.7
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 007785 52 KEDLRRVMELL-SLREHHARTLLIHYRWDVEKLLAVLVE 89 (590)
Q Consensus 52 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~e~l~~~~~~ 89 (590)
.+.+..+++++ +++...++..|..++++++..++.+.+
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 45788899999 899999999999999999999988764
No 108
>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=67.11 E-value=18 Score=25.17 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=27.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHH
Q 007785 54 DLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLV 88 (590)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~ 88 (590)
.|+++.+ +|.+...++..|..++||+++..+.++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4555555 589999999999999999999877654
No 109
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=67.08 E-value=3.1 Score=33.33 Aligned_cols=34 Identities=26% Similarity=0.715 Sum_probs=13.7
Q ss_pred cCCCCCCcceee---cCCCCeeEec-cCce----eecccccc
Q 007785 277 KPCPKCHKPVEK---NGGCNLVSCI-CGQA----FCWLCGGA 310 (590)
Q Consensus 277 K~CPkC~~~IEK---n~GCNHMtC~-Cg~~----FCwlC~~~ 310 (590)
-+|++|...+.. .+||-|++|. |=.. -|-+|-.+
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 589999887765 3788887773 4322 26666554
No 110
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=66.57 E-value=7.7 Score=40.72 Aligned_cols=87 Identities=20% Similarity=0.381 Sum_probs=52.3
Q ss_pred cccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHH
Q 007785 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKF 192 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 192 (590)
...-++||||++.+.. ..+..+=||..|.+|-.. ..-+||. |...++ .++.+.-
T Consensus 45 ~~~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g--~~R~~am---------- 98 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG--NIRCRAM---------- 98 (299)
T ss_pred chhhccCchhhccCcc-cceecCCCcEehhhhhhh-----------hcccCCc--cccccc--cHHHHHH----------
Confidence 3456899999998652 334445589999999762 2358998 988776 3454433
Q ss_pred HHHHhhhhhhcCcccccCCC-CCCCCceEeecCcccceeec
Q 007785 193 ERFLLESFIEDNKMVKWCPS-TPHCGNAIRVEEVEVCEVEC 232 (590)
Q Consensus 193 ~~~l~~~~v~~~~~~~~CP~-~p~C~~~i~~~~~~~~~v~C 232 (590)
+.++++ ....||+ .-+|...+.+.......-.|
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 122222 2345663 24777777665533333344
No 111
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.56 E-value=3.7 Score=42.29 Aligned_cols=43 Identities=26% Similarity=0.776 Sum_probs=33.0
Q ss_pred cccccccccccccCceec-CCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
..|+.|-..+. ++... .|+|.||..|+..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhh--CcccCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 78999988754 55555 89999999999876654 3479998 654
No 112
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.40 E-value=5.8 Score=28.10 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=21.2
Q ss_pred ccCCCCCCCCceEeecCc----ccceeecc-CCCee
Q 007785 208 KWCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-Cg~~f 238 (590)
.-|| +|+..+.++++ ....|.|+ |++.|
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 79999987763 34578996 98876
No 113
>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=66.38 E-value=2.4 Score=39.52 Aligned_cols=9 Identities=33% Similarity=0.626 Sum_probs=4.4
Q ss_pred ccccccccc
Q 007785 116 TVMCDICME 124 (590)
Q Consensus 116 ~~~C~IC~e 124 (590)
..+|||=-+
T Consensus 126 Eg~CPIVIe 134 (167)
T PF05320_consen 126 EGTCPIVIE 134 (167)
T ss_pred cCCCcEEEe
Confidence 345555443
No 114
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.97 E-value=5.9 Score=27.93 Aligned_cols=28 Identities=29% Similarity=0.797 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceEeecC----cccceeecc-CCCee
Q 007785 208 KWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQF 238 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-Cg~~f 238 (590)
.-|| +|+..+.+++ .....+.|+ |++.|
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 3587 7999988766 344578996 98876
No 115
>PHA03096 p28-like protein; Provisional
Probab=65.80 E-value=3.2 Score=43.23 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=29.1
Q ss_pred cccccccccccc----cCcee-c-CCCCccchhhHHHHHHhhh
Q 007785 117 VMCDICMEEVAG----DKATK-M-DCGHCFCNDCWTEHFIVKI 153 (590)
Q Consensus 117 ~~C~IC~e~~~~----~~~~~-l-~CgH~FC~~C~~~yi~~~I 153 (590)
..|.||++.+.. +..+. | .|.|.||..|++.+..+..
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 789999998543 22333 3 8999999999999998865
No 116
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.42 E-value=5.5 Score=29.49 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=19.5
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCceeec
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAFCW 305 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~FCw 305 (590)
-.||+|+..++-..+=..++|. ||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 4689998888765443367884 8776543
No 117
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=65.05 E-value=17 Score=25.18 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHH
Q 007785 54 DLRRVMELLSLREHHARTLLIHYRWDVEKLLAVL 87 (590)
Q Consensus 54 ~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~ 87 (590)
.|+++.++ |.+...|+..|...+||+++..+-+
T Consensus 4 ~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 34444444 8999999999999999999876643
No 118
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.43 E-value=5.3 Score=40.98 Aligned_cols=54 Identities=24% Similarity=0.535 Sum_probs=39.5
Q ss_pred ccccccccccccccccCceecC--CCCccchhhHHHHHHhhhhcCCcccccccc-ccccc
Q 007785 114 SSTVMCDICMEEVAGDKATKMD--CGHCFCNDCWTEHFIVKINEGQSKRIRCMA-HKCNA 170 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~--CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~-~~C~~ 170 (590)
+....|.+|-+-+....++..+ =.|.||.-|-++.|+.+-..|. +.||. .+|..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sge---vYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGE---VYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCc---eeCCCCCcCcc
Confidence 3568999999987644444332 2599999999999998665554 88986 46764
No 119
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.24 E-value=3.9 Score=36.50 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=25.1
Q ss_pred ccCCCCCCCCceEeecC-------cccceeecc-CCCeeecCccCcCCC
Q 007785 208 KWCPSTPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (590)
..|- +|...+.... .......|+ |+..||..|-.-+|.
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 112346796 999999999887775
No 120
>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=63.09 E-value=6 Score=27.59 Aligned_cols=31 Identities=19% Similarity=0.450 Sum_probs=24.8
Q ss_pred CCCCCCc-ceeecCCCCeeEe-ccCceeeccccccccCCC
Q 007785 278 PCPKCHK-PVEKNGGCNLVSC-ICGQAFCWLCGGATGRDH 315 (590)
Q Consensus 278 ~CPkC~~-~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~~~H 315 (590)
.||.|.. ++. ++| .|+...|..|....+++|
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 5889977 888 999 599999999986534444
No 121
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=61.61 E-value=3.6 Score=43.02 Aligned_cols=85 Identities=26% Similarity=0.610 Sum_probs=45.2
Q ss_pred CCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHHHHHH-hhhhhhc----CcccccCC
Q 007785 137 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIED----NKMVKWCP 211 (590)
Q Consensus 137 gH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l-~~~~v~~----~~~~~~CP 211 (590)
|-+||..|-..+.. .|+.||. |...+ +.+ +.+...|..+. ++.|.+. ..+...|-
T Consensus 275 ~Gy~CP~CkakvCs--------LP~eCpi--C~ltL-------Vss---~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf 334 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCS--------LPIECPI--CSLTL-------VSS---PHLARSYHHLFPLKPFVEIPETEYNGSRFCF 334 (378)
T ss_pred CceeCCcccCeeec--------CCccCCc--cceeE-------ecc---hHHHHHHHhhcCCcchhhccccccCCCccee
Confidence 34577777544432 5778887 66432 112 44444554332 2233322 22334465
Q ss_pred CCCCCCceEeecCcccceeecc-CCCeeecCccCcCCC
Q 007785 212 STPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHS 248 (590)
Q Consensus 212 ~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (590)
.|+.- ......+.|. |...||..|..-.|.
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 46221 1223347895 999999999876554
No 122
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=61.50 E-value=1.9e+02 Score=29.51 Aligned_cols=99 Identities=11% Similarity=0.224 Sum_probs=67.4
Q ss_pred cccchHHHHHHHHHHHHHHHhhhccccceeecccccchhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCC
Q 007785 383 RLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYP 462 (590)
Q Consensus 383 ~~~~~~~l~~a~~~l~~~R~vL~~SY~~ayy~~~~~~~~~~~~~~~~~~~~~lfe~~Q~~lE~~~E~Ls~~le~~~~~~~ 462 (590)
+++++-.+..|++.++.-|..+...|... .+.-...+.. +.-.+..-+.+|..+|..+..|..++.++.
T Consensus 140 ~Lkeyv~y~~slK~vlk~R~~~Q~~le~k----------~e~l~k~~~d-r~~~~~ev~~~e~kve~a~~~~k~e~~Rf~ 208 (243)
T cd07666 140 VIHEYVLYSETLMGVIKRRDQIQAELDSK----------VEALANKKAD-RDLLKEEIEKLEDKVECANNALKADWERWK 208 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777788899999999887666544332 0000000111 134444556677777777778888888877
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007785 463 DDKVMEIRMQVINLSVITDTLCKKMYECIE 492 (590)
Q Consensus 463 ~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (590)
.+...++|.-++.++..--.++++++..-|
T Consensus 209 ~~k~~D~k~~~~~yae~~i~~~~~~~~~We 238 (243)
T cd07666 209 QNMQTDLRSAFTDMAENNISYYEECLATWE 238 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 778888898888888888888888888776
No 123
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=60.44 E-value=16 Score=39.15 Aligned_cols=48 Identities=23% Similarity=0.609 Sum_probs=36.9
Q ss_pred cccccccccccccc--cCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 115 STVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 115 ~~~~C~IC~e~~~~--~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
....|..|-+.+.. +....|+|.|.|...|+.+|+.. ++ +-.||. |+.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HHH
Confidence 45789999998653 45567899999999999999943 33 358988 773
No 124
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.18 E-value=4.7 Score=40.68 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=18.4
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCceeecccc
Q 007785 278 PCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCG 308 (590)
Q Consensus 278 ~CPkC~~~IEKn~GCNHMtC-~Cg~~FCwlC~ 308 (590)
.|+.+... .+++| .|+...|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEecccccccCCCCC
Confidence 45555544 56999 59999999998
No 125
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=59.01 E-value=6.6 Score=27.55 Aligned_cols=27 Identities=37% Similarity=0.943 Sum_probs=17.3
Q ss_pred ccCCCCCCCCceEeecCcccceeecc-CCCe
Q 007785 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (590)
++|| .|++.+....+....+.|. |++.
T Consensus 2 ~FCp---~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP---ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BET---TTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCC---CCCccceEcCCCccCcCCCCCCCc
Confidence 5798 7999998766444333674 7665
No 126
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.69 E-value=7 Score=45.33 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=9.9
Q ss_pred CcCCCCCCccee
Q 007785 276 TKPCPKCHKPVE 287 (590)
Q Consensus 276 tK~CPkC~~~IE 287 (590)
.+.||+|+..+-
T Consensus 41 ~~fC~~CG~~~~ 52 (645)
T PRK14559 41 EAHCPNCGAETG 52 (645)
T ss_pred cccccccCCccc
Confidence 489999998876
No 127
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=58.34 E-value=5.2 Score=47.28 Aligned_cols=26 Identities=42% Similarity=1.136 Sum_probs=22.6
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCceee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAFC 304 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~FC 304 (590)
..||.|+..+...+|| ++|+ ||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC--~~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGC--VVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCC--CcCCCCCCCCC
Confidence 3599999999999999 5995 999766
No 128
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=58.31 E-value=4.1 Score=31.61 Aligned_cols=44 Identities=27% Similarity=0.689 Sum_probs=29.8
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
...|-.|... ....+.++|||..|..||-.- .---||. |...+.
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~ 50 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFE 50 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChh----------hccCCCC--CCCccc
Confidence 3556666654 235667899999999998542 1236888 776654
No 129
>cd07630 BAR_SNX_like The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of uncharacterized proteins with similarity to sorting nexins (SNXs), which are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=57.33 E-value=83 Score=31.00 Aligned_cols=99 Identities=12% Similarity=0.216 Sum_probs=64.1
Q ss_pred ccchHHHHHHHHHHHHHHHhhhccccceeecccccchhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCc
Q 007785 384 LRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPD 463 (590)
Q Consensus 384 ~~~~~~l~~a~~~l~~~R~vL~~SY~~ayy~~~~~~~~~~~~~~~~~~~~~lfe~~Q~~lE~~~E~Ls~~le~~~~~~~~ 463 (590)
+.++.-+..|++.++..|.-..-+|--+ + .. ..+.+..++..-|..|+.++..-|.+|..+..++..+..
T Consensus 95 L~~Y~r~i~a~K~~l~~R~~~~~~~~~a-----~----k~-l~Kar~~k~~~ae~~~~~a~~~fe~iS~~~k~EL~rF~~ 164 (198)
T cd07630 95 LDLYSRYSESEKDMLFRRTCKLIEFENA-----S----KA-LEKAKPQKKEQAEEAKKKAETEFEEISSLAKKELERFHR 164 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----H----HH-HHHhHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556667777777776554333333222 0 11 122334556678888899999999999999998887766
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007785 464 DKVMEIRMQVINLSVITDTLCKKMYECIE 492 (590)
Q Consensus 464 ~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (590)
+-+..+|.-++.++...-.+-++.++.+.
T Consensus 165 ~Rv~~fk~~l~~~~E~~i~~ak~~~~~~~ 193 (198)
T cd07630 165 QRVLELQSALVCYAESQIKNAKEAAAVLT 193 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66777777777766666666666655544
No 130
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.96 E-value=2.6 Score=40.47 Aligned_cols=29 Identities=34% Similarity=0.981 Sum_probs=21.7
Q ss_pred cCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee
Q 007785 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
.||+.||..|-+. ...++..||-|++-|.
T Consensus 150 kCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 150 KCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 5999999998652 1235589999998665
No 131
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=56.80 E-value=3.6 Score=34.54 Aligned_cols=12 Identities=42% Similarity=0.570 Sum_probs=0.0
Q ss_pred CCcccCCCCCCc
Q 007785 9 EDYYYSDRDSLD 20 (590)
Q Consensus 9 ~~~~~~~~~~~~ 20 (590)
+|+|+||+++|+
T Consensus 36 ddd~~DDD~dDd 47 (81)
T PF14812_consen 36 DDDYEDDDDDDD 47 (81)
T ss_dssp ------------
T ss_pred ccccccccccch
Confidence 333445555444
No 132
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=56.75 E-value=1.3 Score=37.03 Aligned_cols=47 Identities=32% Similarity=0.432 Sum_probs=33.7
Q ss_pred eCHHHHHHHHHHHHHHHHHHhC--C-CHHHHHHHHHHcCCChHHHHHHHHh
Q 007785 42 ITRESLLAAQKEDLRRVMELLS--L-REHHARTLLIHYRWDVEKLLAVLVE 89 (590)
Q Consensus 42 lt~~~i~~~~~~~i~~v~~~l~--i-~~~~a~~LL~~~~W~~e~l~~~~~~ 89 (590)
||+++-. .+..-+.+|.++|| + +.....-.|.||.+++++.+..+..
T Consensus 20 Ls~ed~~-~L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 20 LSPEDQA-QLYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp -TCHHHH-HHCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCHHHHH-HHHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 4444443 37777888999997 4 5567788899999999999888775
No 133
>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=56.66 E-value=9 Score=26.03 Aligned_cols=26 Identities=27% Similarity=0.722 Sum_probs=12.5
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCcee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~F 303 (590)
-.||+|+....-.+|.+ |.| .|+++|
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 36999998877766654 678 488875
No 134
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=55.63 E-value=8.3 Score=33.39 Aligned_cols=28 Identities=36% Similarity=0.765 Sum_probs=21.0
Q ss_pred CCCCCCcce--eecCCCCeeEec-cCceeec
Q 007785 278 PCPKCHKPV--EKNGGCNLVSCI-CGQAFCW 305 (590)
Q Consensus 278 ~CPkC~~~I--EKn~GCNHMtC~-Cg~~FCw 305 (590)
-||.|+..+ ++.+-||...|+ |.|.|=-
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 699998654 455559999995 9987644
No 135
>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=55.35 E-value=10 Score=31.02 Aligned_cols=32 Identities=41% Similarity=0.970 Sum_probs=21.0
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCc-----eeeccccccc
Q 007785 278 PCPKCHKPVEKNGGCNLVSC-ICGQ-----AFCWLCGGAT 311 (590)
Q Consensus 278 ~CPkC~~~IEKn~GCNHMtC-~Cg~-----~FCwlC~~~~ 311 (590)
.||.|+.+++.++ .+.+| .|+. -+|--|+.+.
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 5885 4699998774
No 136
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=54.97 E-value=4.1 Score=39.87 Aligned_cols=32 Identities=31% Similarity=0.731 Sum_probs=23.7
Q ss_pred CcCCCCCCcceeecCCCCeeEeccCceeecccccccc
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 312 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~~ 312 (590)
.-.||-|...+.. -+.=.|||-|||.|...|-
T Consensus 18 ~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 3589999887641 1333699999999998863
No 137
>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=54.84 E-value=13 Score=26.09 Aligned_cols=27 Identities=33% Similarity=0.870 Sum_probs=19.0
Q ss_pred cCCCCCCCCceEeecCc----ccceeecc-CCCee
Q 007785 209 WCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 238 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~~----~~~~v~C~-Cg~~f 238 (590)
-|| +|+..+.+.++ ....+.|+ |++.|
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 23368886 88765
No 138
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.02 E-value=10 Score=45.53 Aligned_cols=35 Identities=34% Similarity=0.679 Sum_probs=21.9
Q ss_pred hhcCcccccCCCCCCCCceEeecCcccceeecc-CCC-----eeecCccCc
Q 007785 201 IEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGA-----QFCFSCLSE 245 (590)
Q Consensus 201 v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~-----~fC~~C~~~ 245 (590)
++.....+.|| .|+... ....|+ ||. .||..|+..
T Consensus 620 ~eVEVg~RfCp---sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 620 IEVEIGRRKCP---SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred eeecccCccCC---CCCCcC-------CcccCCCCCCCCCcceeCccccCc
Confidence 33444567888 688763 235786 875 477777553
No 139
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.91 E-value=9 Score=38.05 Aligned_cols=54 Identities=20% Similarity=0.413 Sum_probs=41.0
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
..|..|-..+...+.+.|.|-|.|.-.|+.+.-..--.+..-...+||. |...+
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 4699999988888999999999999999998754432222224578998 87644
No 140
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=53.89 E-value=3.3 Score=34.21 Aligned_cols=48 Identities=25% Similarity=0.575 Sum_probs=33.6
Q ss_pred ccccccccccc---------cC-ceec-CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 118 MCDICMEEVAG---------DK-ATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 118 ~C~IC~e~~~~---------~~-~~~l-~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
+|.||--.|+. ++ +..+ .|.|.|..-|+.+++.+.-++| .||. |++.+
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 77777766653 22 1222 6899999999999998866654 5888 77643
No 141
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=53.66 E-value=9.3 Score=28.94 Aligned_cols=26 Identities=27% Similarity=0.604 Sum_probs=14.8
Q ss_pred CcCCCCCCcceeecCCCCeeEe-ccCc
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQ 301 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC-~Cg~ 301 (590)
-+.||+|+.-+--..-=+...| +||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 3789999853332111125677 6775
No 142
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=53.05 E-value=4 Score=47.16 Aligned_cols=30 Identities=30% Similarity=0.867 Sum_probs=21.7
Q ss_pred cCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee
Q 007785 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
.|+|.||+.|-.. .+....+.||+|+.+.-
T Consensus 660 kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-------------------------RYETRQRKCPKCNAAFG 689 (698)
T ss_pred hcchHHHHHHHHH-------------------------HHHHhcCCCCCCCCCCC
Confidence 4999999999753 11223489999998764
No 143
>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=52.76 E-value=12 Score=30.01 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=19.1
Q ss_pred CCcCCCCCCcceeecCCCCeeEec-cCce
Q 007785 275 HTKPCPKCHKPVEKNGGCNLVSCI-CGQA 302 (590)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCNHMtC~-Cg~~ 302 (590)
.++.||.|+....++..=..++|. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 468999999999974333456663 6554
No 144
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=52.52 E-value=6.2 Score=46.65 Aligned_cols=52 Identities=21% Similarity=0.458 Sum_probs=36.9
Q ss_pred ccccccccccccccccC---ce-e-cCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 114 SSTVMCDICMEEVAGDK---AT-K-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~---~~-~-l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
+...+|+||+..+...+ |. + -.|.|.|...|+-.|+...- .-+||. |+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--cccccc
Confidence 34568999999865321 21 2 26999999999999998732 258998 876543
No 145
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=52.23 E-value=3.6 Score=43.02 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=21.5
Q ss_pred CcCCCCCCcceee-cCCCCeeEe-ccCcee
Q 007785 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (590)
Q Consensus 276 tK~CPkC~~~IEK-n~GCNHMtC-~Cg~~F 303 (590)
|..||+|+..|-+ .-.=|.+.| +|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 5899999988864 445567889 599988
No 146
>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=51.70 E-value=4.8e+02 Score=30.99 Aligned_cols=48 Identities=13% Similarity=0.240 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHH
Q 007785 432 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVIT 480 (590)
Q Consensus 432 ~~~lfe~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~ 480 (590)
+.+-..+.|+.|+..++.+...+......+...| ++++.++..+...+
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AE-r~~~~EL~~~~~~l 648 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAE-REFKKELERMKDQL 648 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHH-HHHHHHHHHHHHHH
Confidence 4567778899999999999999876555555443 34444444444433
No 147
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.47 E-value=11 Score=44.21 Aligned_cols=34 Identities=29% Similarity=0.819 Sum_probs=28.7
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCce-----eecccccc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQA-----FCWLCGGA 310 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~-----FCwlC~~~ 310 (590)
-.||+|..++.-...=|.|.|. ||++ .|.-||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4799999988866666899995 9987 89999987
No 148
>PF14369 zf-RING_3: zinc-finger
Probab=50.02 E-value=14 Score=25.90 Aligned_cols=28 Identities=29% Similarity=0.883 Sum_probs=19.3
Q ss_pred ccCCCCCCCCceEeecCcccceeecc-CCCee
Q 007785 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQF 238 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~f 238 (590)
-||- .|...|.........+.|| |+..|
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 4897 7999999754333345686 87655
No 149
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.89 E-value=11 Score=34.62 Aligned_cols=24 Identities=46% Similarity=1.148 Sum_probs=18.5
Q ss_pred CcCCCCCCcceeecCCCCeeEeccCceeecccc
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCG 308 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~ 308 (590)
.+.||.|+.|+.+- -|.-||-+|+
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 37899999999753 4467777777
No 150
>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=49.55 E-value=9.2 Score=33.98 Aligned_cols=25 Identities=32% Similarity=0.874 Sum_probs=16.2
Q ss_pred cCCCCCCccee-ecCCCCeeEe-ccCcee
Q 007785 277 KPCPKCHKPVE-KNGGCNLVSC-ICGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IE-Kn~GCNHMtC-~Cg~~F 303 (590)
+.||+|++..- .|- +.++| +||..|
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 67999987654 232 56777 476655
No 151
>smart00336 BBOX B-Box-type zinc finger.
Probab=49.24 E-value=16 Score=25.78 Aligned_cols=33 Identities=36% Similarity=0.787 Sum_probs=26.4
Q ss_pred cCCCCCC-cceeecCCCCeeEe-ccCceeeccccccccCCCc
Q 007785 277 KPCPKCH-KPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHT 316 (590)
Q Consensus 277 K~CPkC~-~~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~~~H~ 316 (590)
..|+.|. .++. ++| .|....|..|....+++|.
T Consensus 4 ~~C~~h~~~~~~-------~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred CcCCCCCCCceE-------EECCCCCcccccccChhhcCCCc
Confidence 5799998 8888 999 5999999999866444453
No 152
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.35 E-value=12 Score=29.44 Aligned_cols=6 Identities=67% Similarity=2.084 Sum_probs=3.1
Q ss_pred CCCCCC
Q 007785 278 PCPKCH 283 (590)
Q Consensus 278 ~CPkC~ 283 (590)
.||+|+
T Consensus 29 ~CPnCG 34 (61)
T COG2888 29 PCPNCG 34 (61)
T ss_pred eCCCCC
Confidence 455555
No 153
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.24 E-value=10 Score=40.27 Aligned_cols=44 Identities=25% Similarity=0.609 Sum_probs=30.4
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
+....|.||.+... +..-++|||.-| |.--+- ..+.||. |...+
T Consensus 303 ~~p~lcVVcl~e~~--~~~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPK--SAVFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCCceEEecCCcc--ceeeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 34578999999844 677889999976 644331 1256998 77543
No 154
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.19 E-value=9.9 Score=44.82 Aligned_cols=38 Identities=29% Similarity=0.629 Sum_probs=31.2
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhh
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVK 152 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~ 152 (590)
+...|.+|.-.+-....+..+|||.|..+|+...+..-
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 45789999988766666666999999999999887653
No 155
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.81 E-value=15 Score=45.19 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHH-------HHhhhhhhhc
Q 007785 472 QVINLSVITDTLCKKMYEC-------IENDLLGCLQ 500 (590)
Q Consensus 472 ~~~~l~~~~~~~~~~l~~~-------~e~~l~~~~~ 500 (590)
-+...++.+|.++.++|.. =.++|.|-|.
T Consensus 846 yl~~va~fiDdLL~k~Ygl~~fYn~~~~eDLiGhLv 881 (1337)
T PRK14714 846 YLLKVAKFVDDLLEKFYGLPRFYNVEKREDLVGHLV 881 (1337)
T ss_pred HHHHHHHHHHHHHHHhhCCCcccCCCChhhccceee
Confidence 3455677788887777643 1246776664
No 156
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.76 E-value=7 Score=44.36 Aligned_cols=36 Identities=25% Similarity=0.719 Sum_probs=28.6
Q ss_pred ccccccccccccc--cCceecCCCCccchhhHHHHHHh
Q 007785 116 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIV 151 (590)
Q Consensus 116 ~~~C~IC~e~~~~--~~~~~l~CgH~FC~~C~~~yi~~ 151 (590)
-..|+||+..|-. -.++++.|||..|+-|.......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 3679999887543 36789999999999999876553
No 157
>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=46.74 E-value=16 Score=26.62 Aligned_cols=22 Identities=36% Similarity=1.126 Sum_probs=16.0
Q ss_pred cCCCCCCcceee-cCCCCeeEe-ccC
Q 007785 277 KPCPKCHKPVEK-NGGCNLVSC-ICG 300 (590)
Q Consensus 277 K~CPkC~~~IEK-n~GCNHMtC-~Cg 300 (590)
..||.|+.|+-+ ..| .++| .|+
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 444 4666 353
No 158
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=46.44 E-value=15 Score=38.00 Aligned_cols=47 Identities=30% Similarity=0.619 Sum_probs=36.3
Q ss_pred ccccccccccccccc--cCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 114 SSTVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~--~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
+....||||.+.+.. ..+..++|||..-..|+..++.. . +.||. |..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 345679999998542 34556799999999999998764 2 79998 876
No 159
>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=46.32 E-value=17 Score=40.98 Aligned_cols=34 Identities=26% Similarity=0.677 Sum_probs=23.8
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCce-----eecccccc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~-----FCwlC~~~ 310 (590)
-.||+|..++.--..=|.+.| .||+. .|-.|+..
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 478888877763333347889 48866 68888775
No 160
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.21 E-value=13 Score=37.63 Aligned_cols=37 Identities=14% Similarity=0.221 Sum_probs=31.8
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhc
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE 155 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~ 155 (590)
-.|+.|+..+. +++..+=||.||+.|+-+||..+-++
T Consensus 44 dcCsLtLqPc~--dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 44 DCCSLTLQPCR--DPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ceeeeeccccc--CCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 46899998866 78888999999999999999887654
No 161
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=45.85 E-value=4.8 Score=30.54 Aligned_cols=33 Identities=30% Similarity=0.793 Sum_probs=27.6
Q ss_pred cccccccccccccccCceec-CCCCccchhhHHH
Q 007785 115 STVMCDICMEEVAGDKATKM-DCGHCFCNDCWTE 147 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l-~CgH~FC~~C~~~ 147 (590)
..++|..|-+.++..+.... -||-.-|..||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 46899999999887665554 7999999999986
No 162
>cd07621 BAR_SNX5_6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Members of this subfamily include SNX5, SNX6, the mammalian SNX32, and similar proteins. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. The function of SNX32 is still unknown. BAR domain
Probab=45.58 E-value=1.5e+02 Score=29.81 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 007785 436 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDL 495 (590)
Q Consensus 436 fe~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l 495 (590)
-|..|.+++..-|.+|+.+..++..+....+..+|.-++.++..--.+-+..+..+.+-|
T Consensus 156 AE~~~~~a~~~Fe~iS~~~k~El~rF~~~Rv~~fk~~lve~aE~~ik~Ak~~~~~l~~~~ 215 (219)
T cd07621 156 AEAAQQEACEKFESMSESAKQELLDFKTRRVAAFRKNLVELAELEIKHAKAQIQLLKNCL 215 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566788888999999999999998887788999999999999999888888888877544
No 163
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=45.21 E-value=5 Score=41.93 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=14.3
Q ss_pred cCCCCCCcceee-cCCCCeeEe-ccCcee
Q 007785 277 KPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEK-n~GCNHMtC-~Cg~~F 303 (590)
.+||+|+..|-+ .-.=|...| .|+|+|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 566666666543 223444556 366543
No 164
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=45.18 E-value=19 Score=26.87 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=23.1
Q ss_pred cccccccccccCceecCCC--C---ccchhhHHHHHHh
Q 007785 119 CDICMEEVAGDKATKMDCG--H---CFCNDCWTEHFIV 151 (590)
Q Consensus 119 C~IC~e~~~~~~~~~l~Cg--H---~FC~~C~~~yi~~ 151 (590)
|-||++....+.+...||+ - .....|+..|+..
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 7799998665554555665 2 6788999999987
No 165
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.38 E-value=15 Score=45.23 Aligned_cols=56 Identities=27% Similarity=0.380 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHH-hhcccCCC---CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 007785 440 QQQLEANVEKLSKF-LEEPFDQY---PDDKVMEIRMQVINLSVITDTLCKKMYECIENDLL 496 (590)
Q Consensus 440 Q~~lE~~~E~Ls~~-le~~~~~~---~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~ 496 (590)
=..+--.+|+|.++ -++++... .++.|.++|.+=+-|+.-...|+-+.-+.|. +||
T Consensus 799 p~Eigvs~eklreLGY~~Di~G~pL~~~dQivELk~QDiil~~~aa~yl~~va~fiD-dLL 858 (1337)
T PRK14714 799 PREIGVSVEKLRELGYTQDIHGDPLVHEDQVVELKVQDIVLSDGAAEYLLKVAKFVD-DLL 858 (1337)
T ss_pred HHHcCCCHHHHHHcCCccccCCCCCCCccceEEeecccEEcchHHHHHHHHHHHHHH-HHH
Confidence 34556677777776 23343322 2344666666656677777777777777774 444
No 166
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=43.92 E-value=25 Score=25.91 Aligned_cols=29 Identities=31% Similarity=0.871 Sum_probs=20.9
Q ss_pred cCCCCCCCCceEeecCcccceeecc-CCCeeecC
Q 007785 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~ 241 (590)
.|| +|+..+....... .+.|+ ||..+=..
T Consensus 5 ~C~---~CG~~~~~~~~~~-~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 5 KCA---RCGREVELDEYGT-GVRCPYCGYRILFK 34 (46)
T ss_pred ECC---CCCCEEEECCCCC-ceECCCCCCeEEEc
Confidence 587 7999888776543 57897 98876543
No 167
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=43.78 E-value=10 Score=39.12 Aligned_cols=32 Identities=28% Similarity=0.744 Sum_probs=26.1
Q ss_pred cCCCCCCcceeecCCCCeeEe--ccCceeeccccccccCCC
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGATGRDH 315 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC--~Cg~~FCwlC~~~~~~~H 315 (590)
-+|--|.-.|- +-| .|||.||++|-...-..|
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 57989998888 889 499999999988754444
No 168
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=43.68 E-value=10 Score=32.95 Aligned_cols=32 Identities=19% Similarity=0.494 Sum_probs=24.3
Q ss_pred cccccccccccccccccCceecCCCCccchhh
Q 007785 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144 (590)
Q Consensus 113 ~~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C 144 (590)
....|+|.-||-....+....-.=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45789999999886655544445589999998
No 169
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=43.64 E-value=8.3 Score=40.09 Aligned_cols=53 Identities=26% Similarity=0.611 Sum_probs=37.7
Q ss_pred CcccccCCCCCCCCceEeecCcccceeeccCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCC
Q 007785 204 NKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCH 283 (590)
Q Consensus 204 ~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~ 283 (590)
+..+.+|- .|+..|.+=+.- =+|.+.||..|-.. |. .|.||.|.
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 44567786 798877643211 15999999999752 21 18999999
Q ss_pred cceeecCCC
Q 007785 284 KPVEKNGGC 292 (590)
Q Consensus 284 ~~IEKn~GC 292 (590)
-.|+|.+-|
T Consensus 131 d~VqrIeq~ 139 (389)
T KOG2932|consen 131 DRVQRIEQI 139 (389)
T ss_pred cHHHHHHHh
Confidence 999987755
No 170
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=43.49 E-value=16 Score=40.02 Aligned_cols=21 Identities=29% Similarity=0.480 Sum_probs=12.6
Q ss_pred CCCCCCccccccccccccccc
Q 007785 107 ADPMLPLSSTVMCDICMEEVA 127 (590)
Q Consensus 107 ~~~~~~~~~~~~C~IC~e~~~ 127 (590)
..+..|.++.|.|.-==++-+
T Consensus 185 ~tP~LPDSTDFVCGTLDEDRP 205 (458)
T PF10446_consen 185 GTPELPDSTDFVCGTLDEDRP 205 (458)
T ss_pred CCCCCCCcccccCCCcCCcch
Confidence 344556677788876444444
No 171
>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=43.33 E-value=5.8 Score=41.34 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=20.0
Q ss_pred CcCCCCCCcceeec-CCCCeeEe-ccCcee
Q 007785 276 TKPCPKCHKPVEKN-GGCNLVSC-ICGQAF 303 (590)
Q Consensus 276 tK~CPkC~~~IEKn-~GCNHMtC-~Cg~~F 303 (590)
|..||+|+..|-+. -.=|.+.| .|+++|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 57899999888653 34456788 488875
No 172
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=43.21 E-value=13 Score=40.72 Aligned_cols=6 Identities=0% Similarity=-0.009 Sum_probs=2.5
Q ss_pred HHHHHH
Q 007785 346 YMHYHN 351 (590)
Q Consensus 346 y~~y~~ 351 (590)
|..|+.
T Consensus 407 ~rk~C~ 412 (458)
T PF10446_consen 407 WRKHCR 412 (458)
T ss_pred HHHHHH
Confidence 344443
No 173
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=43.16 E-value=21 Score=26.69 Aligned_cols=27 Identities=37% Similarity=0.888 Sum_probs=17.1
Q ss_pred ccCCCCCCCCceEeecCccc-ceeecc-CCCe
Q 007785 208 KWCPSTPHCGNAIRVEEVEV-CEVECA-CGAQ 237 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~~ 237 (590)
++|| .|+..+....... ....|+ ||+.
T Consensus 1 ~FCp---~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 1 KFCP---KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCC---CCCCccccccCCCCCEEECCcCCCe
Confidence 3688 7999887654322 356675 7754
No 174
>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=42.87 E-value=39 Score=30.28 Aligned_cols=42 Identities=24% Similarity=0.592 Sum_probs=29.0
Q ss_pred CCcCCCCCCcceeecCCCCeeEe-ccCceeeccccccccCCCcc
Q 007785 275 HTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTW 317 (590)
Q Consensus 275 ~tK~CPkC~~~IEKn~GCNHMtC-~Cg~~FCwlC~~~~~~~H~w 317 (590)
+.+.|..|+.+.-.-.+.. ..| .|++.+|-.|+........|
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 5679999998865544444 889 59999999999873334444
No 175
>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=42.70 E-value=21 Score=27.25 Aligned_cols=11 Identities=45% Similarity=0.942 Sum_probs=8.5
Q ss_pred cCCCCCCccee
Q 007785 277 KPCPKCHKPVE 287 (590)
Q Consensus 277 K~CPkC~~~IE 287 (590)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 89999986544
No 176
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.27 E-value=19 Score=42.00 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=22.4
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCce----eecccccc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQA----FCWLCGGA 310 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~----FCwlC~~~ 310 (590)
-.||+|..++.-..+=+.+.|. ||+. .|-.|++.
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 4788888777654444568884 8753 47777664
No 177
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=41.85 E-value=1.6e+02 Score=29.61 Aligned_cols=62 Identities=16% Similarity=0.255 Sum_probs=46.2
Q ss_pred HHHHH--HHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 007785 432 KQHLF--EDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIEN 493 (590)
Q Consensus 432 ~~~lf--e~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~ 493 (590)
.+++- |..|.+.+..-|++|+.+..++..+...-+..+|.-++.++...=.+-+.-+..+.+
T Consensus 149 ~kev~~aE~~~~~a~~~Fe~IS~~aK~El~rF~~~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~~~ 212 (218)
T cd07662 149 NKDVLQAETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQLLQS 212 (218)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444 778888899999999999988877666667777877777777776666666666553
No 178
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.70 E-value=23 Score=34.09 Aligned_cols=57 Identities=25% Similarity=0.487 Sum_probs=37.9
Q ss_pred ccccccccccc-cccc--C--ceecCCCCccchhhHHHHHHhhhhcCCcccc---cccccccccccc
Q 007785 115 STVMCDICMEE-VAGD--K--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRI---RCMAHKCNAICD 173 (590)
Q Consensus 115 ~~~~C~IC~e~-~~~~--~--~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i---~CP~~~C~~~~~ 173 (590)
....|.||+-- ++.. + .-...||..|..-|+..|+..-+...+++.| .||- |..++.
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 44567777753 1111 1 1234799999999999999988777666554 5877 766543
No 179
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.56 E-value=7.2 Score=39.77 Aligned_cols=36 Identities=22% Similarity=0.266 Sum_probs=24.5
Q ss_pred cccccccccc-cccc-cCcee-cCCCCccchhhHHHHHH
Q 007785 115 STVMCDICME-EVAG-DKATK-MDCGHCFCNDCWTEHFI 150 (590)
Q Consensus 115 ~~~~C~IC~e-~~~~-~~~~~-l~CgH~FC~~C~~~yi~ 150 (590)
...++++++. ++.. .++.. -.|||.||..|-.-++.
T Consensus 94 ~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~ 132 (271)
T COG5574 94 REETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSI 132 (271)
T ss_pred cccccccccCcccccccccceeeecccccchhhhHHHHH
Confidence 5678999988 4322 23333 38999999999665554
No 180
>PF12773 DZR: Double zinc ribbon
Probab=41.40 E-value=11 Score=28.21 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=8.1
Q ss_pred cCCCCCCcceee
Q 007785 277 KPCPKCHKPVEK 288 (590)
Q Consensus 277 K~CPkC~~~IEK 288 (590)
+.||+|+..+..
T Consensus 30 ~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 30 KICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCCcC
Confidence 667777776654
No 181
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=41.28 E-value=7.2 Score=44.99 Aligned_cols=50 Identities=26% Similarity=0.625 Sum_probs=37.9
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccch
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 174 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~ 174 (590)
..+|+||+..+- +++.+.|.|.||..||..-+...-. ...||. |+..+..
T Consensus 21 ~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK 70 (684)
T KOG4362|consen 21 ILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEK 70 (684)
T ss_pred hccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhh
Confidence 478999999865 5678899999999999987765322 467887 7755443
No 182
>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=41.10 E-value=18 Score=31.50 Aligned_cols=24 Identities=33% Similarity=0.804 Sum_probs=17.6
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCce
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~ 302 (590)
+.||+|+.++...+ +.+.| .|++.
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCc
Confidence 36999999887654 37888 47775
No 183
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=41.07 E-value=13 Score=30.85 Aligned_cols=54 Identities=22% Similarity=0.633 Sum_probs=20.3
Q ss_pred CCCceEeecCcccceeecc-CCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCcceeecCCCC
Q 007785 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (590)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCN 293 (590)
-|+--|.........|-|. |+...|..|.. +. ++..++.||+|+.+..+..|+.
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 5777777666666778895 99998887643 21 2234589999999988777754
No 184
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.99 E-value=23 Score=30.17 Aligned_cols=29 Identities=28% Similarity=0.687 Sum_probs=22.2
Q ss_pred CcCCCCCCcceeecCCCCeeEe-ccCceee
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSC-ICGQAFC 304 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC-~Cg~~FC 304 (590)
--.||.|+++.-|..+=---.| +||+.|=
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 3689999999888776666777 4887763
No 185
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=40.85 E-value=19 Score=41.76 Aligned_cols=47 Identities=32% Similarity=0.607 Sum_probs=36.2
Q ss_pred cccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
..+.|.||.-.+.....+...|+|....+|...||.. |. .||. ||+.
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~----gd----~Cps-GCGC 1073 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT----GD----VCPS-GCGC 1073 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc----CC----cCCC-CCCc
Confidence 4567999987777666677799999999999999986 32 6885 3443
No 186
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.51 E-value=18 Score=42.60 Aligned_cols=40 Identities=20% Similarity=0.578 Sum_probs=30.6
Q ss_pred cccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
..|..|--++.. +++...|||.|...|+. ++. -.||. |..
T Consensus 841 skCs~C~~~Ldl-P~VhF~CgHsyHqhC~e--------~~~---~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDL-PFVHFLCGHSYHQHCLE--------DKE---DKCPK--CLP 880 (933)
T ss_pred eeecccCCcccc-ceeeeecccHHHHHhhc--------cCc---ccCCc--cch
Confidence 579999877552 45667999999999998 333 68987 775
No 187
>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=40.12 E-value=53 Score=39.21 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=14.6
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 007785 68 HARTLLIHYRWDVEKLLAVL 87 (590)
Q Consensus 68 ~a~~LL~~~~W~~e~l~~~~ 87 (590)
.++..++|||-.+=.|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 57778888877777776665
No 188
>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=39.13 E-value=12 Score=28.59 Aligned_cols=22 Identities=27% Similarity=0.772 Sum_probs=13.0
Q ss_pred ceeecc-CCCeeecCccCcCCCC
Q 007785 228 CEVECA-CGAQFCFSCLSEAHSP 249 (590)
Q Consensus 228 ~~v~C~-Cg~~fC~~C~~~~H~p 249 (590)
....|+ |+..||+.|-.-.|.-
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 457896 9999999998766753
No 189
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=39.12 E-value=18 Score=28.89 Aligned_cols=37 Identities=22% Similarity=0.548 Sum_probs=19.3
Q ss_pred ccccccccccccccccC-ceec-CCCCccchhhHHHHHH
Q 007785 114 SSTVMCDICMEEVAGDK-ATKM-DCGHCFCNDCWTEHFI 150 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~-~~~l-~CgH~FC~~C~~~yi~ 150 (590)
.+...|.+|...|..-. -... .||+.||.+|....+.
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEc
Confidence 45678999999986422 1222 7999999999866543
No 190
>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=37.71 E-value=39 Score=25.75 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 007785 53 EDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (590)
Q Consensus 53 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~ 89 (590)
+.|..++...|++..-+...|...+||.++.+..|.+
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 5678899999999999999999999999999998874
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=37.70 E-value=1.3e+02 Score=24.06 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 007785 49 AAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVE 89 (590)
Q Consensus 49 ~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~ 89 (590)
..|++.|..++...|++...+..+|-..+||.+..+..|.+
T Consensus 10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45778889999999999999999999999999998888764
No 192
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=37.69 E-value=11 Score=32.60 Aligned_cols=10 Identities=20% Similarity=0.125 Sum_probs=4.3
Q ss_pred HHHHHHHHHh
Q 007785 53 EDLRRVMELL 62 (590)
Q Consensus 53 ~~i~~v~~~l 62 (590)
+-+..|...|
T Consensus 51 ~~~~~v~rYl 60 (101)
T PF09026_consen 51 AYFTMVKRYL 60 (101)
T ss_dssp HHHHHHHHHH
T ss_pred hhcchHhhhh
Confidence 3344444444
No 193
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.68 E-value=27 Score=40.97 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=23.9
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCce-----eecccccc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA-----FCWLCGGA 310 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~-----FCwlC~~~ 310 (590)
-.||+|..++.--..=|.+.| .||+. .|-.|++.
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 478888888763333356889 49876 58888775
No 194
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=37.67 E-value=3.7e+02 Score=31.77 Aligned_cols=63 Identities=11% Similarity=0.128 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCC----CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 007785 434 HLFEDQQQQLEANVEKLSKFLEEPFDQ----YPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLL 496 (590)
Q Consensus 434 ~lfe~~Q~~lE~~~E~Ls~~le~~~~~----~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~ 496 (590)
.+|..+-.++....+.|.+.+.+--.. +....-..+-.++.++.+.+.+++.-+|+.++..++
T Consensus 272 ~vFr~l~~q~~~m~esver~~~kl~~~~~~~~~~~~~~~l~~~i~s~~~k~~~~~~~I~ka~~~sIi 338 (683)
T PF08580_consen 272 IVFRNLGRQAQKMCESVERSLSKLQEAIDSGIHLDNPSKLSKQIESKEKKKSHYFPAIYKARVLSII 338 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccccccchHHHHHHHHHHHHHHhccHHHHHHHHHHHhh
Confidence 466666666666666555554421111 011111234456666666666666666666554433
No 195
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=37.35 E-value=19 Score=43.94 Aligned_cols=17 Identities=29% Similarity=0.628 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q 007785 436 FEDQQQQLEANVEKLSK 452 (590)
Q Consensus 436 fe~~Q~~lE~~~E~Ls~ 452 (590)
||..|....+.+|+|..
T Consensus 2419 FEtKer~Fnka~EK~Rn 2435 (3015)
T KOG0943|consen 2419 FETKERKFNKAMEKLRN 2435 (3015)
T ss_pred cchHHHHHHHHHHHHHh
Confidence 56666666666666554
No 196
>PHA02926 zinc finger-like protein; Provisional
Probab=37.08 E-value=11 Score=37.73 Aligned_cols=35 Identities=29% Similarity=0.730 Sum_probs=23.2
Q ss_pred cCCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee
Q 007785 233 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 233 ~Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
+|+|.||+.|-..| ..... + ....+.||-|+....
T Consensus 196 ~CnHsFCl~CIr~W------------r~~r~-~-------~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 196 SCNHIFCITCINIW------------HRTRR-E-------TGASDNCPICRTRFR 230 (242)
T ss_pred CCCchHHHHHHHHH------------HHhcc-c-------cCcCCcCCCCcceee
Confidence 49999999997754 32111 1 012378999998775
No 197
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.02 E-value=26 Score=27.20 Aligned_cols=32 Identities=28% Similarity=0.858 Sum_probs=25.6
Q ss_pred cccccccccccc-ccCceec-CCCCccchhhHHH
Q 007785 116 TVMCDICMEEVA-GDKATKM-DCGHCFCNDCWTE 147 (590)
Q Consensus 116 ~~~C~IC~e~~~-~~~~~~l-~CgH~FC~~C~~~ 147 (590)
...|++|-+.|. .++.+.. .||-.|.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 457999999985 4566665 8999999999965
No 198
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.94 E-value=25 Score=30.80 Aligned_cols=27 Identities=26% Similarity=0.693 Sum_probs=16.3
Q ss_pred CcCCCCCCcce---eecCCCCeeEe-ccCce
Q 007785 276 TKPCPKCHKPV---EKNGGCNLVSC-ICGQA 302 (590)
Q Consensus 276 tK~CPkC~~~I---EKn~GCNHMtC-~Cg~~ 302 (590)
.-.||+|+... ....|=-|+.| .||+.
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 22335557777 47765
No 199
>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=36.71 E-value=35 Score=25.86 Aligned_cols=46 Identities=17% Similarity=0.465 Sum_probs=24.1
Q ss_pred cccccccccccccCce-ecCCCCccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 117 VMCDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~-~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
..|+|-+..+. -++ ...|.|.-|.+ +..|+....+.+. .+||. |..
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 56888887654 344 45999998854 7788887766554 79998 653
No 200
>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=36.08 E-value=1.4e+02 Score=26.22 Aligned_cols=48 Identities=25% Similarity=0.290 Sum_probs=38.4
Q ss_pred eCHHHHHH-----HHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhc
Q 007785 42 ITRESLLA-----AQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVEN 90 (590)
Q Consensus 42 lt~~~i~~-----~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~l~~~~~~~ 90 (590)
.++++|+. .++++|-.+++-+.++..+|.+||. ..=-.+.|++.|...
T Consensus 24 qpPeeIl~~AYEy~VkeDi~m~~ee~~l~~~qa~ALl~-sp~PL~~iY~~w~~~ 76 (101)
T PF12959_consen 24 QPPEEILNHAYEYTVKEDILMAMEELELPDQQAKALLK-SPSPLADIYREWEKK 76 (101)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHc-CCChHHHHHHHHHhc
Confidence 46778876 5788999999999999999999996 455567788888753
No 201
>PRK12495 hypothetical protein; Provisional
Probab=36.06 E-value=39 Score=33.74 Aligned_cols=18 Identities=22% Similarity=0.672 Sum_probs=15.3
Q ss_pred CCcCCCCCCcceeecCCC
Q 007785 275 HTKPCPKCHKPVEKNGGC 292 (590)
Q Consensus 275 ~tK~CPkC~~~IEKn~GC 292 (590)
..+.||.|+.||-+..||
T Consensus 41 sa~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ 58 (226)
T ss_pred chhhcccccCcccCCCCe
Confidence 357999999999987776
No 202
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=35.66 E-value=26 Score=23.34 Aligned_cols=24 Identities=29% Similarity=0.778 Sum_probs=13.0
Q ss_pred cCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 277 KPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 277 K~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
++||+|..+|++ .+|=+...| +|.
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 589999999975 345555566 454
No 203
>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=35.59 E-value=28 Score=26.22 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=16.8
Q ss_pred CcCCC--CCCcceeecCCCCeeEe-ccCc
Q 007785 276 TKPCP--KCHKPVEKNGGCNLVSC-ICGQ 301 (590)
Q Consensus 276 tK~CP--kC~~~IEKn~GCNHMtC-~Cg~ 301 (590)
-+.|| +|+.-+--..=-+..+| +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 47899 99987653333466788 7875
No 204
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=34.46 E-value=13 Score=38.24 Aligned_cols=28 Identities=29% Similarity=0.670 Sum_probs=21.1
Q ss_pred CcCCCCCCcceee-cCCCCeeEe-ccCcee
Q 007785 276 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 303 (590)
Q Consensus 276 tK~CPkC~~~IEK-n~GCNHMtC-~Cg~~F 303 (590)
|..||.|+..+-+ .-+=|...| +|+|+|
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 5789999988864 446677788 588775
No 205
>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=34.45 E-value=29 Score=25.42 Aligned_cols=41 Identities=27% Similarity=0.630 Sum_probs=19.9
Q ss_pred cccccccccccCce-ecCCCCccchhhHHHHHHhhhhcCCcccccccc
Q 007785 119 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 165 (590)
Q Consensus 119 C~IC~e~~~~~~~~-~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~ 165 (590)
|.+|-+.+.....- ...|+=.+...|+..||...-. .+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~------~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSN------PKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-------B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCC------CCCcC
Confidence 67787765522111 1258889999999999986321 27886
No 206
>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=34.16 E-value=29 Score=30.73 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=16.2
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCcee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~F 303 (590)
-.||+|..-..=..|= .+.|. |+|+|
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCC-eeECccccccc
Confidence 4799998766655553 35553 55554
No 207
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=34.13 E-value=34 Score=23.88 Aligned_cols=27 Identities=33% Similarity=0.872 Sum_probs=13.2
Q ss_pred ccCCCCCCCCceEee---cCcccceeecc-CCCe
Q 007785 208 KWCPSTPHCGNAIRV---EEVEVCEVECA-CGAQ 237 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~---~~~~~~~v~C~-Cg~~ 237 (590)
++|| .|+..+.. .++......|+ ||+.
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 79998764 33555567785 8764
No 208
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.66 E-value=16 Score=40.71 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=19.1
Q ss_pred CcCCCCCCcceeecCCCCeeEe--ccCceeecccccc
Q 007785 276 TKPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGA 310 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCNHMtC--~Cg~~FCwlC~~~ 310 (590)
-..||-|-.+-. .-+ .|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 368999987665 334 2777777777543
No 209
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=33.59 E-value=24 Score=32.39 Aligned_cols=51 Identities=25% Similarity=0.531 Sum_probs=37.4
Q ss_pred cccccccccccccccCceec--CCCCccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~l--~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
.-.+|.||-|.......... -||=..|.-|....|...- ....||. |+..+
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 45899999998542222222 5999999999999998753 3468998 87654
No 210
>PRK11827 hypothetical protein; Provisional
Probab=32.59 E-value=38 Score=26.85 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=17.6
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCc
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQ 301 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~ 301 (590)
-.||.|+.+++-..+=+.+.|+ |+-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 5899999998865554556663 553
No 211
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.53 E-value=30 Score=35.71 Aligned_cols=25 Identities=44% Similarity=1.075 Sum_probs=17.8
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 3799999999986 566555555 354
No 212
>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=32.21 E-value=40 Score=22.38 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.0
Q ss_pred CCCCCCcceeecCCCCeeEe
Q 007785 278 PCPKCHKPVEKNGGCNLVSC 297 (590)
Q Consensus 278 ~CPkC~~~IEKn~GCNHMtC 297 (590)
.||.|+..+.+..|=-+++|
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 49999999999888667776
No 213
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=31.52 E-value=32 Score=35.64 Aligned_cols=25 Identities=40% Similarity=1.060 Sum_probs=20.4
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++|+.|+.+|+| -+|=+-.+| .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 3799999999997 578877888 476
No 214
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=31.51 E-value=1.6e+02 Score=30.76 Aligned_cols=31 Identities=19% Similarity=0.316 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 007785 334 KKTERAKRELYRYMHYHNRYKAHTDSFKLES 364 (590)
Q Consensus 334 ~~~~~~k~~l~ry~~y~~r~~~h~~s~k~e~ 364 (590)
.+..++-+.|++|.+-++|-.+....+.+|.
T Consensus 151 ~ranQAi~TLEkYk~~Ld~~~~~L~~lEled 181 (349)
T COG1623 151 SRANQAIQTLEKYKTVLDRVLNQLNLLELED 181 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhHHHhh
Confidence 5678888999999999998877777766664
No 215
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=31.32 E-value=28 Score=36.81 Aligned_cols=32 Identities=25% Similarity=0.753 Sum_probs=24.6
Q ss_pred ccccccccccccccccCceecCCCCccchhhHHH
Q 007785 114 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 147 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~ 147 (590)
.+...|.||...++ -...+||+|..|.-|--.
T Consensus 59 Een~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~R 90 (493)
T COG5236 59 EENMNCQICAGSTT--YSARYPCGHQICHACAVR 90 (493)
T ss_pred cccceeEEecCCce--EEEeccCCchHHHHHHHH
Confidence 35678999998865 334569999999999644
No 216
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=31.26 E-value=2.9e+02 Score=22.59 Aligned_cols=45 Identities=27% Similarity=0.358 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHH
Q 007785 435 LFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLC 484 (590)
Q Consensus 435 lfe~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~ 484 (590)
-|+.+++..+.....|...++.. ..+-..++.++.+|+.-|..+=
T Consensus 18 ~y~~q~~~Wq~sy~~Lq~~~~~t-----~~~~a~L~~qv~~Ls~qv~~Ls 62 (70)
T PF04899_consen 18 SYEKQQQEWQSSYADLQHMFEQT-----SQENAALSEQVNNLSQQVQRLS 62 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh-----HHHHHHHHHHHHHHHHHHHHHH
Confidence 57777778888888888887743 2334566777777777665443
No 217
>PHA02929 N1R/p28-like protein; Provisional
Probab=31.17 E-value=20 Score=36.34 Aligned_cols=38 Identities=24% Similarity=0.407 Sum_probs=26.2
Q ss_pred CcCCCCCCcceeecCCCC---eeEeccCceeeccccccccC
Q 007785 276 TKPCPKCHKPVEKNGGCN---LVSCICGQAFCWLCGGATGR 313 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GCN---HMtC~Cg~~FCwlC~~~~~~ 313 (590)
...||-|.-.+.....-+ -+.-.|+|.||..|...|..
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 13446888999999888654
No 218
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=31.13 E-value=44 Score=26.84 Aligned_cols=14 Identities=43% Similarity=0.949 Sum_probs=10.8
Q ss_pred CCcCCCCCCcceee
Q 007785 275 HTKPCPKCHKPVEK 288 (590)
Q Consensus 275 ~tK~CPkC~~~IEK 288 (590)
+.|+||-|+..+..
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 45999999876654
No 219
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=31.10 E-value=33 Score=35.44 Aligned_cols=25 Identities=40% Similarity=1.024 Sum_probs=18.7
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 3699999999986 566666666 365
No 220
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.61 E-value=1.8e+02 Score=28.96 Aligned_cols=61 Identities=15% Similarity=0.119 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhhhhhc-ccccc-CCCCCCCCccccccccccccccCCCC
Q 007785 466 VMEIRMQVINLSVITDTLCKKMYECIEN---DLLGCLQ-LGTHN-IARYQSKGIERASELSTCWTSVNTTT 531 (590)
Q Consensus 466 i~~~k~~~~~l~~~~~~~~~~l~~~~e~---~l~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 (590)
|.+...+|.+|-+-+.. ++.-|+ ++|+.+- .+++. ++|..+--|-++...+..|.+...+.
T Consensus 57 Lk~a~~~i~eLe~ri~~-----lq~~~~~sgsFLs~~f~~gt~~e~app~~a~~p~~~aap~S~rs~~~g~ 122 (233)
T COG3416 57 LKKASTQIKELEKRIAI-----LQAGEAGSGSFLSNAFKWGTPQEPAPPANAPPPKEPAAPPSWRSSPAGP 122 (233)
T ss_pred HHHHHHHHHHHHHHHHH-----HhcccCCCcchhhhhcccCCCCCCCCCcCCCCCCCCCCCCCccccccCC
Confidence 55556666655555522 222233 2343331 23444 67666644555677888887766553
No 221
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.54 E-value=41 Score=35.24 Aligned_cols=50 Identities=18% Similarity=0.491 Sum_probs=35.5
Q ss_pred ccccccccccccc-ccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccc
Q 007785 115 STVMCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 171 (590)
Q Consensus 115 ~~~~C~IC~e~~~-~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~ 171 (590)
+.|+|||=-+..+ .+.|+.|.|||..=+.=+... -++|. ..++||- |+..
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~L----S~nG~-~~FKCPY--CP~~ 385 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVL----SQNGV-LSFKCPY--CPEM 385 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHH----hhcCc-EEeeCCC--CCcc
Confidence 5689999777643 356788899999887665543 23555 5789998 8754
No 222
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.46 E-value=35 Score=35.30 Aligned_cols=24 Identities=42% Similarity=1.013 Sum_probs=18.1
Q ss_pred cCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 277 KPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 277 K~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
++||.|+.+|+| .+|=.-.+| .|+
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 699999999986 567666666 363
No 223
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=30.22 E-value=54 Score=22.72 Aligned_cols=12 Identities=33% Similarity=0.515 Sum_probs=9.0
Q ss_pred CcCCCCCCccee
Q 007785 276 TKPCPKCHKPVE 287 (590)
Q Consensus 276 tK~CPkC~~~IE 287 (590)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 378999987665
No 224
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=30.02 E-value=26 Score=42.77 Aligned_cols=8 Identities=38% Similarity=0.467 Sum_probs=3.1
Q ss_pred CCCCccee
Q 007785 280 PKCHKPVE 287 (590)
Q Consensus 280 PkC~~~IE 287 (590)
|+|-.-+.
T Consensus 2282 ~kclfE~r 2289 (3015)
T KOG0943|consen 2282 GKCLFEVR 2289 (3015)
T ss_pred CcceEEEe
Confidence 34433333
No 225
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.99 E-value=35 Score=35.29 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=18.8
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++||+|+.+|++ .+|=.-.+| .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 4799999999986 567655666 465
No 226
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.79 E-value=35 Score=35.41 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=19.4
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 3799999999986 577666777 465
No 227
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=29.37 E-value=20 Score=30.47 Aligned_cols=35 Identities=29% Similarity=0.503 Sum_probs=28.6
Q ss_pred cCCCCCCcceeecCCCCeeEeccCceeeccccccccCC
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRD 314 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~~~~ 314 (590)
.-||.|+.| ...|--+.+.|++.|=..|...|-..
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 45788888899999999999987543
No 228
>PRK10445 endonuclease VIII; Provisional
Probab=28.57 E-value=40 Score=34.71 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=19.0
Q ss_pred CcCCCCCCcceee--cCCCCeeEe-ccC
Q 007785 276 TKPCPKCHKPVEK--NGGCNLVSC-ICG 300 (590)
Q Consensus 276 tK~CPkC~~~IEK--n~GCNHMtC-~Cg 300 (590)
-++||.|+.+|++ .+|=.-.+| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 3799999999986 567666666 465
No 229
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=28.05 E-value=18 Score=37.64 Aligned_cols=89 Identities=25% Similarity=0.490 Sum_probs=47.2
Q ss_pred CCccchhhHHHHHHhhhhcCCcccccccccccccccchHHHHHHhcCCCchHHHHHHHH-HhhhhhhcC----cccccCC
Q 007785 137 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERF-LLESFIEDN----KMVKWCP 211 (590)
Q Consensus 137 gH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~-l~~~~v~~~----~~~~~CP 211 (590)
|-++|..|-..-. ..||.||. |... -+++ ..+...|..+ -++.+++.. +....|-
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 4567777743322 25788886 5432 2333 3444555443 234455433 2334454
Q ss_pred CCCCCCceEeecC-------cccceeecc-CCCeeecCccCcCCC
Q 007785 212 STPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 248 (590)
Q Consensus 212 ~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H~ 248 (590)
.|+..+.... .......|. |...||..|..-.|.
T Consensus 367 ---~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 367 ---VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ---eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 4655444322 112346896 999999999765553
No 230
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.91 E-value=38 Score=40.92 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=24.0
Q ss_pred hCCcCCCCCCcceeecCCCCeeEec-cCc-----eeecccccc
Q 007785 274 VHTKPCPKCHKPVEKNGGCNLVSCI-CGQ-----AFCWLCGGA 310 (590)
Q Consensus 274 ~~tK~CPkC~~~IEKn~GCNHMtC~-Cg~-----~FCwlC~~~ 310 (590)
...+.||.|+... ....|. ||. .||-.|+..
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 599999765
No 231
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=27.79 E-value=3.8e+02 Score=27.90 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 007785 468 EIRMQVINLSVITDTLCKKM 487 (590)
Q Consensus 468 ~~k~~~~~l~~~~~~~~~~l 487 (590)
+.|.+|.+|-.+|++-..+|
T Consensus 121 EARkEIkQLkQvieTmrssL 140 (305)
T PF15290_consen 121 EARKEIKQLKQVIETMRSSL 140 (305)
T ss_pred HHHHHHHHHHHHHHHHHhhh
Confidence 33333333433333333333
No 232
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.35 E-value=43 Score=34.14 Aligned_cols=53 Identities=15% Similarity=0.341 Sum_probs=37.9
Q ss_pred cccccccccccccccCcee---cCCC-----CccchhhHHHHHHhhhhcCCccccccccccccc
Q 007785 115 STVMCDICMEEVAGDKATK---MDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 170 (590)
Q Consensus 115 ~~~~C~IC~e~~~~~~~~~---l~Cg-----H~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~ 170 (590)
.+-.|=|||..-.. +... -||. |....+|+..|+..+-..+...++.||+ |..
T Consensus 19 ~eR~CWiCF~TdeD-n~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqT 79 (293)
T KOG3053|consen 19 LERCCWICFATDED-NRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQT 79 (293)
T ss_pred cceeEEEEeccCcc-cchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcc
Confidence 45689999987332 2222 2564 6789999999999887644456899999 875
No 233
>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=27.27 E-value=35 Score=31.17 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=16.1
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCcee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~F 303 (590)
+.||+|++..---.- +-++| +||..|
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 689999876542111 55777 476653
No 234
>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=27.17 E-value=59 Score=30.86 Aligned_cols=36 Identities=28% Similarity=0.572 Sum_probs=23.3
Q ss_pred ccccccccccccccCceecC-------CCCccc------hhhHHHHHHhhh
Q 007785 116 TVMCDICMEEVAGDKATKMD-------CGHCFC------NDCWTEHFIVKI 153 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~-------CgH~FC------~~C~~~yi~~~I 153 (590)
..+|+||++- +-+.+.|- |.-+.| .+|+.+|-....
T Consensus 2 d~~CpICme~--PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEH--PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccC--CCceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 4689999986 23555553 333444 478888876554
No 235
>PLN02189 cellulose synthase
Probab=26.88 E-value=38 Score=41.13 Aligned_cols=60 Identities=28% Similarity=0.612 Sum_probs=42.2
Q ss_pred cCCCCCCCCceEeecCcccceeecc-CCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCccee
Q 007785 209 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 287 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IE 287 (590)
-|. -|+--+....+....|-|. |+...|..|-+- . . +...+.||.|+....
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 465 5877777666666779996 999999988631 0 0 123489999999988
Q ss_pred ecCCCCeeE
Q 007785 288 KNGGCNLVS 296 (590)
Q Consensus 288 Kn~GCNHMt 296 (590)
+--|++.+.
T Consensus 88 r~kgs~~v~ 96 (1040)
T PLN02189 88 RLKGSPRVE 96 (1040)
T ss_pred hccCCCCcC
Confidence 766666543
No 236
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=26.76 E-value=63 Score=32.09 Aligned_cols=16 Identities=31% Similarity=0.837 Sum_probs=12.7
Q ss_pred ccCCCCCCCCceEeecC
Q 007785 208 KWCPSTPHCGNAIRVEE 224 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~ 224 (590)
.-|| .|+|.++|....
T Consensus 139 IACP-RpnCkRiInL~p 154 (275)
T KOG4684|consen 139 IACP-RPNCKRIINLDP 154 (275)
T ss_pred eccC-CCCcceeeecCC
Confidence 4799 799999988643
No 237
>PRK10220 hypothetical protein; Provisional
Probab=26.36 E-value=49 Score=29.40 Aligned_cols=26 Identities=23% Similarity=0.700 Sum_probs=15.4
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCcee
Q 007785 277 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC~-Cg~~F 303 (590)
-.||+|..-..=..|= .+.|. |+|+|
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 5899998766544442 34552 55443
No 238
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=26.36 E-value=58 Score=24.67 Aligned_cols=28 Identities=32% Similarity=0.596 Sum_probs=18.1
Q ss_pred CcCCCCCCcceeecCCC--------CeeEeccCcee
Q 007785 276 TKPCPKCHKPVEKNGGC--------NLVSCICGQAF 303 (590)
Q Consensus 276 tK~CPkC~~~IEKn~GC--------NHMtC~Cg~~F 303 (590)
.-.||+|+--.--|++= -+=+|+||..+
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfni 48 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFNI 48 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeecccccc
Confidence 36899999776655443 23467777643
No 239
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=26.31 E-value=3.1e+02 Score=30.09 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 007785 431 IKQHLFEDQQQQLEANVEKLSKFLE 455 (590)
Q Consensus 431 ~~~~lfe~~Q~~lE~~~E~Ls~~le 455 (590)
..++.||...+..-..++.|.+.||
T Consensus 48 rIkq~FekkNqksa~~i~~lqkkL~ 72 (395)
T PF10267_consen 48 RIKQVFEKKNQKSAQTIAQLQKKLE 72 (395)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 4456666655555556666665555
No 240
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.72 E-value=52 Score=29.44 Aligned_cols=27 Identities=26% Similarity=0.594 Sum_probs=18.2
Q ss_pred cCCCCCCcceee--cCCCCeeEe-ccCcee
Q 007785 277 KPCPKCHKPVEK--NGGCNLVSC-ICGQAF 303 (590)
Q Consensus 277 K~CPkC~~~IEK--n~GCNHMtC-~Cg~~F 303 (590)
+.||+|+.++.- .++=+-+.| +||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 689999987764 112226888 488764
No 241
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=25.46 E-value=47 Score=38.93 Aligned_cols=48 Identities=15% Similarity=0.357 Sum_probs=32.6
Q ss_pred ccccccccccccccCc-eecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccc
Q 007785 116 TVMCDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 173 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~-~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~ 173 (590)
.-.|++|+..+..... ....|+|.||..|+..|-... -.||. |...+.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~ 171 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFG 171 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhhh
Confidence 3468888877543222 234899999999999986541 37887 665554
No 242
>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=24.71 E-value=80 Score=24.50 Aligned_cols=27 Identities=41% Similarity=0.815 Sum_probs=20.1
Q ss_pred cCCCCCCCCceEeecC-cccceeecc-CCCee
Q 007785 209 WCPSTPHCGNAIRVEE-VEVCEVECA-CGAQF 238 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~-~~~~~v~C~-Cg~~f 238 (590)
-|| .|+.-|.+.+ ...-.+.|+ ||..+
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 243
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.18 E-value=55 Score=24.99 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=23.5
Q ss_pred ccccccccccccCceecCCCCccchhhHHHH
Q 007785 118 MCDICMEEVAGDKATKMDCGHCFCNDCWTEH 148 (590)
Q Consensus 118 ~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~y 148 (590)
.|+||-..+..-..+.+.=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999998765444667777 8999999876
No 244
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=24.11 E-value=6.9e+02 Score=24.54 Aligned_cols=97 Identities=15% Similarity=0.289 Sum_probs=53.1
Q ss_pred ccccchHHHHHHHHHHHHHHHhhhccccceeecccccchhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCC
Q 007785 382 SRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQY 461 (590)
Q Consensus 382 ~~~~~~~~l~~a~~~l~~~R~vL~~SY~~ayy~~~~~~~~~~~~~~~~~~~~~lfe~~Q~~lE~~~E~Ls~~le~~~~~~ 461 (590)
.+++++.....+++.+++.|....+.|... .+..+.+...++..-+.+....+...+.+..++..+
T Consensus 98 e~LkEy~~ya~slk~vlk~r~~~q~~~e~~--------------~~~L~~k~~~l~~~ve~a~~~~e~f~~~~~~E~~rF 163 (201)
T cd07622 98 DQLKEYLFFADSLRAVCKKHELLQYDLEKA--------------EDALANKKQQGEEAVKEAKDELNEFVKKALEDVERF 163 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357788888889999998787777755443 111112222222222222222222222333444444
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007785 462 PDDKVMEIRMQVINLSVITDTLCKKMYECIE 492 (590)
Q Consensus 462 ~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 492 (590)
...+..++|.-+.+++..=-.++++++..-+
T Consensus 164 ~~~K~~dlk~~l~~~A~~qi~~~~~~~~~W~ 194 (201)
T cd07622 164 KKQKVRDLKEILISYAKLQIKLAKKGLQTWT 194 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667777777777776667777766554
No 245
>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=24.06 E-value=33 Score=26.25 Aligned_cols=25 Identities=28% Similarity=0.647 Sum_probs=13.0
Q ss_pred cCCCCCCcceeecCCC--CeeEe-ccCc
Q 007785 277 KPCPKCHKPVEKNGGC--NLVSC-ICGQ 301 (590)
Q Consensus 277 K~CPkC~~~IEKn~GC--NHMtC-~Cg~ 301 (590)
-+|++|++.+-+.++= -.|.| +|+.
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 3566666666553222 23556 4553
No 246
>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=24.03 E-value=27 Score=27.24 Aligned_cols=44 Identities=23% Similarity=0.544 Sum_probs=30.2
Q ss_pred cccccccccccccCceecCCC--CccchhhHHHHHHhhhhcCCccccccccccccccc
Q 007785 117 VMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 172 (590)
Q Consensus 117 ~~C~IC~e~~~~~~~~~l~Cg--H~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~ 172 (590)
..|..|-.+++.+..-..-|. ..||.+|-...+. -.||. |+..+
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 358888888876554444454 5799999887753 26887 77644
No 247
>PF14149 YhfH: YhfH-like protein
Probab=23.84 E-value=6.3 Score=28.06 Aligned_cols=26 Identities=31% Similarity=0.790 Sum_probs=20.1
Q ss_pred hCCcCCCCCCcceeecCCCCeeEe-cc
Q 007785 274 VHTKPCPKCHKPVEKNGGCNLVSC-IC 299 (590)
Q Consensus 274 ~~tK~CPkC~~~IEKn~GCNHMtC-~C 299 (590)
...|.||.|+..|+--.-|-.+.| +|
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 346999999999987766766777 45
No 248
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=23.59 E-value=15 Score=38.57 Aligned_cols=30 Identities=30% Similarity=0.903 Sum_probs=21.3
Q ss_pred cCCCCCCCCceEeecCcccceeeccCCCeeecCcc
Q 007785 209 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCL 243 (590)
Q Consensus 209 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~ 243 (590)
+|| -|-..+-..+.. .+-|+||+..|..|-
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 598 676555554443 368999999998874
No 249
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.53 E-value=55 Score=31.78 Aligned_cols=25 Identities=36% Similarity=0.844 Sum_probs=20.1
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCcee
Q 007785 278 PCPKCHKPVEKNGGCNLVSC-ICGQAF 303 (590)
Q Consensus 278 ~CPkC~~~IEKn~GCNHMtC-~Cg~~F 303 (590)
.||+|+.++.+ .+.|+|.| .|++..
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEE-CCCCEEECCCCCCEE
Confidence 79999999987 44599999 598653
No 250
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=23.45 E-value=57 Score=23.38 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=17.8
Q ss_pred CCCCCCcceeecCCCCeeEeccCceeeccccccc
Q 007785 278 PCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 311 (590)
Q Consensus 278 ~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~ 311 (590)
.||+|+..++...- ..+. ...|-.|++.|
T Consensus 1 ~CP~C~~~l~~~~~-~~~~----id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDVE----IDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEE-CCEE----EEECCCCCeEE
Confidence 59999998775332 1122 34466777775
No 251
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.43 E-value=45 Score=40.71 Aligned_cols=57 Identities=19% Similarity=0.537 Sum_probs=39.9
Q ss_pred CCCceEeecCcccceeecc-CCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCcceeecCCCC
Q 007785 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (590)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCN 293 (590)
-|+--|....+....|-|. |+.-.|..|-+ +.+ +...+-||+|+....+--||.
T Consensus 22 ICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE----------YEr---------------~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 22 ICGDNVGKTVDGEPFVACDVCAFPVCRPCYE----------YER---------------KDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred ecccccCcCCCCCEEEEeccCCCccccchhh----------hhh---------------hcCCccCCccCCchhhhcCCC
Confidence 5777777666666779996 99999988863 111 123488999999888666665
Q ss_pred eeE
Q 007785 294 LVS 296 (590)
Q Consensus 294 HMt 296 (590)
.+-
T Consensus 77 rv~ 79 (1079)
T PLN02638 77 AIL 79 (1079)
T ss_pred CcC
Confidence 543
No 252
>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=23.38 E-value=95 Score=29.39 Aligned_cols=32 Identities=28% Similarity=0.530 Sum_probs=20.2
Q ss_pred cCcccccCCCCCCCCceEeecCcccceeecc-CCCe
Q 007785 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (590)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (590)
.++.+-.|| .|+.-+...+.-...+.|| ||..
T Consensus 105 ~~~~~Y~Cp---~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICP---NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECC---CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345566898 5876666555433457786 7765
No 253
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.32 E-value=28 Score=33.02 Aligned_cols=29 Identities=17% Similarity=0.523 Sum_probs=21.0
Q ss_pred cccccccccccccccc-CceecCCCCccch
Q 007785 114 SSTVMCDICMEEVAGD-KATKMDCGHCFCN 142 (590)
Q Consensus 114 ~~~~~C~IC~e~~~~~-~~~~l~CgH~FC~ 142 (590)
....+|.||+|++... .+..|+|-..|.+
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 3568899999997654 4556798766653
No 254
>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=22.94 E-value=49 Score=26.68 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=12.8
Q ss_pred ccchhhHHHHHHhhhhcC
Q 007785 139 CFCNDCWTEHFIVKINEG 156 (590)
Q Consensus 139 ~FC~~C~~~yi~~~I~~g 156 (590)
-||++|+..|+...-.+.
T Consensus 11 gFCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEER 28 (68)
T ss_dssp S--HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 499999999998876543
No 255
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=22.54 E-value=1.1e+03 Score=29.28 Aligned_cols=15 Identities=47% Similarity=1.232 Sum_probs=12.0
Q ss_pred CcCCCCCCcceeecC
Q 007785 276 TKPCPKCHKPVEKNG 290 (590)
Q Consensus 276 tK~CPkC~~~IEKn~ 290 (590)
.-.||+|+.|+|-..
T Consensus 796 ~~~~~~~~~~~~~~~ 810 (1006)
T PRK12775 796 VATCPKCHRPLEGDE 810 (1006)
T ss_pred CccCcccCCCCCCCc
Confidence 357999999999543
No 256
>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=22.41 E-value=1.1e+02 Score=36.05 Aligned_cols=40 Identities=23% Similarity=0.254 Sum_probs=25.0
Q ss_pred eEeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHH
Q 007785 39 TKVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEK 82 (590)
Q Consensus 39 ~~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~e~ 82 (590)
++.|++.++.+..++.-..-.+- .+.-..||++-+|..+.
T Consensus 413 f~~l~ksq~~kl~k~q~k~y~de----~dyr~kl~~kkq~ke~~ 452 (763)
T TIGR00993 413 FKPLTKAQMAKLSKEQRKAYLEE----YDYRVKLLQKKQWREEL 452 (763)
T ss_pred CccccHHHHHHHhHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence 46688888877665543322222 24556788888897665
No 257
>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=22.23 E-value=53 Score=23.91 Aligned_cols=26 Identities=27% Similarity=0.677 Sum_probs=14.1
Q ss_pred CCCCceEeecCcccceeecc-CCCeeecCccCc
Q 007785 214 PHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSE 245 (590)
Q Consensus 214 p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~ 245 (590)
++|..... ..+.|+ |+..||.....+
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 46655433 247897 999999997643
No 258
>KOG4759 consensus Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=22.04 E-value=6.5e+02 Score=25.96 Aligned_cols=66 Identities=18% Similarity=0.183 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 007785 432 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLG 497 (590)
Q Consensus 432 ~~~lfe~~Q~~lE~~~E~Ls~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~ 497 (590)
...+|+...+.+-.---+..+.+........++++.++..++.+|+...-+....|++.-|.+|++
T Consensus 197 ~~~~~ee~K~slr~ir~~~~kk~~k~~~~~~~D~vkkae~~l~~l~k~~v~~ld~llkskeKellk 262 (263)
T KOG4759|consen 197 LKRYFEEYKQSLRKIRTKSIKKSKKNKKSLSEDEVKKAEAELQKLAKDAVNKLDDLLKSKEKELLK 262 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344555555555444444444444433347789999999999999999999999999998888874
No 259
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.96 E-value=1.2e+02 Score=28.20 Aligned_cols=19 Identities=26% Similarity=0.560 Sum_probs=13.5
Q ss_pred HHHHHHhCCCHHHHHHHHH
Q 007785 56 RRVMELLSLREHHARTLLI 74 (590)
Q Consensus 56 ~~v~~~l~i~~~~a~~LL~ 74 (590)
..+++.||++....|.+|.
T Consensus 19 edLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 19 EDLAELLGIKQKQLRKILY 37 (147)
T ss_pred HHHHHHhCCCHHHHHHHHH
Confidence 3456677888887777775
No 260
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=21.79 E-value=79 Score=29.07 Aligned_cols=21 Identities=48% Similarity=1.262 Sum_probs=11.3
Q ss_pred cCCCC--CCcceeecCCCCeeEec--cCcee
Q 007785 277 KPCPK--CHKPVEKNGGCNLVSCI--CGQAF 303 (590)
Q Consensus 277 K~CPk--C~~~IEKn~GCNHMtC~--Cg~~F 303 (590)
|.||+ |.-.++ ++-|+ |||-.
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 999998 68884 88643
No 261
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.59 E-value=79 Score=23.36 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=5.1
Q ss_pred cCCCCCCcce
Q 007785 277 KPCPKCHKPV 286 (590)
Q Consensus 277 K~CPkC~~~I 286 (590)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 4555555444
No 262
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.51 E-value=60 Score=31.64 Aligned_cols=24 Identities=33% Similarity=0.960 Sum_probs=16.8
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCce
Q 007785 277 KPCPKCHKPVEKNGGCNLVSC-ICGQA 302 (590)
Q Consensus 277 K~CPkC~~~IEKn~GCNHMtC-~Cg~~ 302 (590)
-.|++|+.++++ .=+.|+| +||+.
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 378888888888 3366777 47754
No 263
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.47 E-value=1.1e+03 Score=26.92 Aligned_cols=78 Identities=14% Similarity=0.302 Sum_probs=42.7
Q ss_pred HHhhhccccceeecccccchhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-cCCCCchHHHHHHHHHHHHHHH
Q 007785 401 RRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEP-FDQYPDDKVMEIRMQVINLSVI 479 (590)
Q Consensus 401 R~vL~~SY~~ayy~~~~~~~~~~~~~~~~~~~~~lfe~~Q~~lE~~~E~Ls~~le~~-~~~~~~~~i~~~k~~~~~l~~~ 479 (590)
+.+|..++.||- ....+|.+-..+|..-.....+.+.. ... ..+-+..++..+..|...
T Consensus 154 k~ll~~~~~~G~-------------------a~~~le~~l~~~e~~f~~f~~l~~~Gd~~~-A~e~l~~l~~~~~~l~~~ 213 (569)
T PRK04778 154 KSLLANRFSFGP-------------------ALDELEKQLENLEEEFSQFVELTESGDYVE-AREILDQLEEELAALEQI 213 (569)
T ss_pred HHHHhcCccccc-------------------hHHHHHHHHHHHHHHHHHHHHHhcCCCHHH-HHHHHHHHHHHHHHHHHH
Confidence 467778888882 22345555555555555555554431 100 112356667777777766
Q ss_pred HHHHHHHHHHHHHhhhhhhh
Q 007785 480 TDTLCKKMYECIENDLLGCL 499 (590)
Q Consensus 480 ~~~~~~~l~~~~e~~l~~~~ 499 (590)
++.. -.||+-+++.||+-|
T Consensus 214 ~~~i-P~l~~~~~~~~P~ql 232 (569)
T PRK04778 214 MEEI-PELLKELQTELPDQL 232 (569)
T ss_pred HHHH-HHHHHHHHHHhhHHH
Confidence 6443 355666666665444
No 264
>PLN02436 cellulose synthase A
Probab=21.23 E-value=57 Score=39.85 Aligned_cols=57 Identities=25% Similarity=0.561 Sum_probs=39.2
Q ss_pred CCCceEeecCcccceeecc-CCCeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCcceeecCCCC
Q 007785 215 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 293 (590)
Q Consensus 215 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCN 293 (590)
-|+--|....+....|-|. |+...|..|-.- . . +...+.||.|+....+--|++
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 5776666555666779996 999999988631 0 0 123478999999888666665
Q ss_pred eeE
Q 007785 294 LVS 296 (590)
Q Consensus 294 HMt 296 (590)
.+.
T Consensus 96 ~~~ 98 (1094)
T PLN02436 96 RVE 98 (1094)
T ss_pred CcC
Confidence 543
No 265
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=21.16 E-value=45 Score=40.00 Aligned_cols=24 Identities=50% Similarity=1.297 Sum_probs=19.0
Q ss_pred cCCCCCCc-ceeecCCCCeeEe-ccCce
Q 007785 277 KPCPKCHK-PVEKNGGCNLVSC-ICGQA 302 (590)
Q Consensus 277 K~CPkC~~-~IEKn~GCNHMtC-~Cg~~ 302 (590)
-.||-|+. .||..|||| +| .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 47999985 788999996 67 47754
No 266
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=21.09 E-value=6.8e+02 Score=27.53 Aligned_cols=90 Identities=22% Similarity=0.297 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHH-HHHHHHHHHHHHhhhhccccchHHHHHHHHHHHH-HHHhhhccccceeeccc
Q 007785 339 AKRELYRYMHYHNRYKAHTDSFKLESK-LKETVLEKVSISEERESRLRDFSWVTNGLYRLFR-SRRVLSYSYPFAFYMFG 416 (590)
Q Consensus 339 ~k~~l~ry~~y~~r~~~h~~s~k~e~~-l~~~i~~k~~~~~~~~~~~~~~~~l~~a~~~l~~-~R~vL~~SY~~ayy~~~ 416 (590)
||.++--...--.|++.|.+.++-+-. |.+.++.+-++.++ |+.-..+|.+ ||.|..-
T Consensus 123 AKDSItSlKekt~~vnQHVq~LQseCsvlsEnLErrrQEaeE----------LEgyCsqLk~nCrkVt~S---------- 182 (558)
T PF15358_consen 123 AKDSITSLKEKTSRVNQHVQTLQSECSVLSENLERRRQEAEE----------LEGYCSQLKENCRKVTRS---------- 182 (558)
T ss_pred cccchhhHHHhhHHHHHHHHHHHHHhHHHHHHHHhhhhHHHH----------HHHHHHHHHHHHHHHhhh----------
Confidence 444444445556788889999888754 44444444444333 4444555554 4544432
Q ss_pred ccchhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 007785 417 EELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEP 457 (590)
Q Consensus 417 ~~~~~~~~~~~~~~~~~~lfe~~Q~~lE~~~E~Ls~~le~~ 457 (590)
-++.+++.+.+..+-..||..+.-|..-|..+
T Consensus 183 ---------VedaEiKtnvLkqnS~~LEekLr~lq~qLqdE 214 (558)
T PF15358_consen 183 ---------VEDAEIKTNVLKQNSALLEEKLRYLQQQLQDE 214 (558)
T ss_pred ---------HHHHHHHhcccccchHHHHHHHHHHHHHhccc
Confidence 12235677788888888888887777777644
No 267
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=21.04 E-value=96 Score=27.07 Aligned_cols=28 Identities=39% Similarity=0.850 Sum_probs=17.8
Q ss_pred ccCCCCCCCCceEeecCccc-ceeecc-CCCee
Q 007785 208 KWCPSTPHCGNAIRVEEVEV-CEVECA-CGAQF 238 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~~f 238 (590)
.+|| .|++.+.++.+.. ..+.|. |++.|
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 3788 7999998876443 445553 55443
No 268
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=20.90 E-value=71 Score=32.45 Aligned_cols=35 Identities=26% Similarity=0.700 Sum_probs=0.0
Q ss_pred hHHHHHhCCcCCCCCCcc-eee---cCCCCeeEe-ccCcee
Q 007785 268 TVNWITVHTKPCPKCHKP-VEK---NGGCNLVSC-ICGQAF 303 (590)
Q Consensus 268 ~~~~i~~~tK~CPkC~~~-IEK---n~GCNHMtC-~Cg~~F 303 (590)
+..|+..|. .||+|+.. +.+ |.-=--..| .|+.+|
T Consensus 24 tE~Wv~~n~-yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 24 TEDWVAENM-YCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp HHHHHHHH----TTT--SS-EE--------EEE-TTT--EE
T ss_pred HHHHHHHCC-cCCCCCChhHhhccCCCccceeECCCCchHH
No 269
>PHA02664 hypothetical protein; Provisional
Probab=20.79 E-value=1.3e+02 Score=31.67 Aligned_cols=13 Identities=31% Similarity=0.447 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHhC
Q 007785 51 QKEDLRRVMELLS 63 (590)
Q Consensus 51 ~~~~i~~v~~~l~ 63 (590)
-.+.+..|.++|+
T Consensus 521 e~~vl~ava~mlg 533 (534)
T PHA02664 521 ERAVLGAVAEMLG 533 (534)
T ss_pred HHHHHHHHHHHhc
Confidence 3455566666664
No 270
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=20.74 E-value=1.1e+03 Score=25.64 Aligned_cols=26 Identities=27% Similarity=0.276 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 007785 430 EIKQHLFEDQQQQLEANVEKLSKFLE 455 (590)
Q Consensus 430 ~~~~~lfe~~Q~~lE~~~E~Ls~~le 455 (590)
+.+.++||.=|+.-+..+.=|.++|-
T Consensus 216 E~MeqvFe~CQ~fE~~Rl~Ffkeil~ 241 (472)
T KOG2856|consen 216 EDMEQVFEQCQQFEEKRLQFFKEILL 241 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35668999988887777766666554
No 271
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.68 E-value=1.1e+02 Score=29.62 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=19.0
Q ss_pred cCcccccCCCCCCCCceEeecCcccceeecc-CCCe
Q 007785 203 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 237 (590)
Q Consensus 203 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 237 (590)
.+..+-.|| .|+.-+...+.-...+.|| ||..
T Consensus 113 ~~~~~Y~Cp---~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 113 ENNMFFFCP---NCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred cCCCEEECC---CCCcEEeHHHHhhcCCcCCCCCCC
Confidence 344566898 5887666555333346665 6544
No 272
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=20.54 E-value=1.2e+03 Score=26.01 Aligned_cols=28 Identities=36% Similarity=0.258 Sum_probs=17.5
Q ss_pred CCccccccCCCCCCCCCCCCCccccccccc
Q 007785 542 SGGTLEHDRPSGSRSSDDSGCSSQKRVRKE 571 (590)
Q Consensus 542 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 571 (590)
.+||.-.-.+++++++ +.-+.+|++|+.
T Consensus 465 qegtI~~~~~s~~~~~--~~~~kkk~nrrk 492 (493)
T KOG0804|consen 465 QEGTILITQISPSSSS--SVKSKKKSNRRK 492 (493)
T ss_pred cCceeeccCCCCCccc--cccchhhhcccC
Confidence 4566666667777665 445566666654
No 273
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.48 E-value=60 Score=25.44 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.6
Q ss_pred CCcCCCCCCccee
Q 007785 275 HTKPCPKCHKPVE 287 (590)
Q Consensus 275 ~tK~CPkC~~~IE 287 (590)
+.-.||+|+.+..
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 4568999999887
No 274
>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=20.42 E-value=92 Score=24.63 Aligned_cols=26 Identities=35% Similarity=0.748 Sum_probs=18.4
Q ss_pred CCCCCCcc----eeecCCCCeeEe-ccCcee
Q 007785 278 PCPKCHKP----VEKNGGCNLVSC-ICGQAF 303 (590)
Q Consensus 278 ~CPkC~~~----IEKn~GCNHMtC-~Cg~~F 303 (590)
.||+|+.. +-+..|=.++.| .|||.-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 79999864 224566688999 598753
No 275
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=20.41 E-value=1.1e+02 Score=24.82 Aligned_cols=31 Identities=32% Similarity=0.623 Sum_probs=22.9
Q ss_pred ccCCCCCCCCceEeecCcccceeecc-CCCeeecC
Q 007785 208 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 241 (590)
Q Consensus 208 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~ 241 (590)
..|| +|++.-.+-......|+|. ||...+.-
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 4688 8998766655555678995 99887754
No 276
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.30 E-value=42 Score=33.49 Aligned_cols=80 Identities=20% Similarity=0.509 Sum_probs=50.9
Q ss_pred CeeecCccCcCCCCCCchhhHHHHHhhhchHHhHHHHHhCCcCCCCCCcceeecCCCCeeEeccCceeeccccccccCCC
Q 007785 236 AQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRDH 315 (590)
Q Consensus 236 ~~fC~~C~~~~H~p~sC~~~~~w~~~~~~e~e~~~~i~~~tK~CPkC~~~IEKn~GCNHMtC~Cg~~FCwlC~~~~~~~H 315 (590)
...|..|....|..+--..+-+|.....- .--|.-|+++++.- .|-.+ .|-+-|=|.|+..|...-
T Consensus 21 VNVCEhClV~nHpkCiVQSYLqWL~DsDY-----------~pNC~LC~t~La~g-dt~RL--vCyhlfHW~ClneraA~l 86 (299)
T KOG3970|consen 21 VNVCEHCLVANHPKCIVQSYLQWLQDSDY-----------NPNCRLCNTPLASG-DTTRL--VCYHLFHWKCLNERAANL 86 (299)
T ss_pred hhHHHHHHhccCchhhHHHHHHHHhhcCC-----------CCCCceeCCccccC-cceee--hhhhhHHHHHhhHHHhhC
Confidence 44577788888987766677777653211 14688899988732 22111 388999999998865433
Q ss_pred cccc-cCCcccCCcc
Q 007785 316 TWSR-IAGHSCGRYK 329 (590)
Q Consensus 316 ~w~~-~~g~~C~~y~ 329 (590)
.-++ -.||.|+.-.
T Consensus 87 PanTAPaGyqCP~Cs 101 (299)
T KOG3970|consen 87 PANTAPAGYQCPCCS 101 (299)
T ss_pred CCcCCCCcccCCCCC
Confidence 2222 3578887543
No 277
>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=20.28 E-value=1.3e+02 Score=22.77 Aligned_cols=45 Identities=18% Similarity=0.410 Sum_probs=23.7
Q ss_pred ccccccccccccccCceecCCCCccchhhHHHHHHhhhhcCCcccccccccccccccchHHH
Q 007785 116 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 177 (590)
Q Consensus 116 ~~~C~IC~e~~~~~~~~~l~CgH~FC~~C~~~yi~~~I~~g~~~~i~CP~~~C~~~~~~~~i 177 (590)
.+.||.|...++.. . +..++...=... ...+.||. |...+....+
T Consensus 2 ~f~CP~C~~~~~~~---~-----------L~~H~~~~H~~~-~~~v~CPi--C~~~~~~~l~ 46 (54)
T PF05605_consen 2 SFTCPYCGKGFSES---S-----------LVEHCEDEHRSE-SKNVVCPI--CSSRVTDNLI 46 (54)
T ss_pred CcCCCCCCCccCHH---H-----------HHHHHHhHCcCC-CCCccCCC--chhhhhhHHH
Confidence 57899998854421 1 223333221111 23689998 8765444333
Done!