Query 008581
Match_columns 561
No_of_seqs 442 out of 1627
Neff 7.6
Searched_HMMs 46136
Date Thu Mar 28 13:58:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008581hhsearch_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 1.7E-71 3.6E-76 597.6 24.4 432 68-523 2-442 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 1.9E-33 4.1E-38 295.0 9.2 218 139-385 145-371 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 3.1E-32 6.6E-37 274.5 7.2 190 137-330 181-405 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.4E-23 3.1E-28 204.5 7.4 189 136-331 217-437 (446)
5 smart00647 IBR In Between Ring 99.3 7.2E-12 1.6E-16 98.3 5.9 63 206-268 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 9.9E-12 2.1E-16 97.5 0.6 63 206-268 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 2E-08 4.3E-13 71.8 1.1 39 143-184 1-41 (42)
8 KOG0320 Predicted E3 ubiquitin 98.1 1E-06 2.2E-11 81.0 0.8 54 136-196 127-182 (187)
9 KOG4367 Predicted Zn-finger pr 98.0 2.1E-05 4.6E-10 81.1 9.2 78 243-329 174-253 (699)
10 smart00647 IBR In Between Ring 98.0 7.3E-06 1.6E-10 64.0 3.9 39 291-330 17-59 (64)
11 PF13445 zf-RING_UBOX: RING-ty 97.9 1.3E-06 2.8E-11 62.6 -0.7 39 143-183 1-43 (43)
12 PF01485 IBR: IBR domain; Int 97.9 2.7E-06 5.8E-11 66.4 0.6 38 292-330 18-59 (64)
13 PLN03208 E3 ubiquitin-protein 97.8 4.7E-06 1E-10 78.7 0.8 58 138-199 16-86 (193)
14 PF13923 zf-C3HC4_2: Zinc fing 97.8 5.4E-06 1.2E-10 58.3 0.7 36 143-184 1-38 (39)
15 PF00097 zf-C3HC4: Zinc finger 97.8 6.4E-06 1.4E-10 58.5 0.6 37 143-184 1-40 (41)
16 KOG0804 Cytoplasmic Zn-finger 97.7 0.0012 2.6E-08 69.1 16.5 116 69-193 86-223 (493)
17 PF13639 zf-RING_2: Ring finge 97.7 5.7E-06 1.2E-10 59.8 -0.7 39 142-184 2-42 (44)
18 PF14634 zf-RING_5: zinc-RING 97.6 1.9E-05 4.1E-10 57.1 1.2 41 142-188 1-43 (44)
19 KOG2177 Predicted E3 ubiquitin 97.6 2.1E-05 4.5E-10 80.1 1.3 44 138-189 11-55 (386)
20 PF13920 zf-C3HC4_3: Zinc fing 97.6 2.3E-05 5E-10 58.3 0.6 45 140-192 2-48 (50)
21 PHA02929 N1R/p28-like protein; 97.4 0.00013 2.8E-09 72.0 4.4 49 138-192 172-227 (238)
22 TIGR00599 rad18 DNA repair pro 97.3 6.9E-05 1.5E-09 79.1 1.3 65 138-210 24-90 (397)
23 cd00162 RING RING-finger (Real 97.3 7.7E-05 1.7E-09 53.2 0.7 42 142-190 1-44 (45)
24 KOG0823 Predicted E3 ubiquitin 97.2 0.00011 2.3E-09 70.9 0.6 55 137-196 44-99 (230)
25 KOG0317 Predicted E3 ubiquitin 97.2 7E-05 1.5E-09 74.3 -0.8 50 139-196 238-288 (293)
26 smart00504 Ubox Modified RING 97.2 0.00015 3.3E-09 56.3 1.2 46 141-195 2-49 (63)
27 KOG0287 Postreplication repair 97.2 0.0001 2.2E-09 74.2 0.2 62 139-209 22-86 (442)
28 PHA02926 zinc finger-like prot 97.0 0.00021 4.6E-09 68.4 0.9 53 138-192 168-230 (242)
29 KOG2164 Predicted E3 ubiquitin 97.0 0.00013 2.8E-09 77.7 -0.8 58 140-201 186-245 (513)
30 smart00184 RING Ring finger. E 96.9 0.00023 5E-09 48.8 0.2 37 143-184 1-38 (39)
31 TIGR00570 cdk7 CDK-activating 96.8 0.00055 1.2E-08 69.6 1.8 52 140-198 3-60 (309)
32 PF14835 zf-RING_6: zf-RING of 96.4 0.0013 2.9E-08 50.7 1.1 43 140-191 7-50 (65)
33 KOG0978 E3 ubiquitin ligase in 96.3 0.00059 1.3E-08 76.1 -1.9 54 138-199 641-696 (698)
34 PF04564 U-box: U-box domain; 96.2 0.0017 3.7E-08 52.3 1.0 49 139-194 3-52 (73)
35 PF14555 UBA_4: UBA-like domai 96.2 0.01 2.2E-07 42.6 4.8 41 79-119 1-41 (43)
36 COG5574 PEX10 RING-finger-cont 96.1 0.0022 4.7E-08 63.1 1.0 52 139-196 214-266 (271)
37 KOG1814 Predicted E3 ubiquitin 95.6 0.0085 1.8E-07 62.4 3.1 42 289-331 270-313 (445)
38 COG5540 RING-finger-containing 95.5 0.0049 1.1E-07 61.5 1.0 51 138-193 321-373 (374)
39 KOG0824 Predicted E3 ubiquitin 95.5 0.0063 1.4E-07 60.9 1.6 51 139-197 6-58 (324)
40 PF11789 zf-Nse: Zinc-finger o 95.4 0.0076 1.6E-07 46.1 1.5 45 139-188 10-57 (57)
41 KOG4628 Predicted E3 ubiquitin 95.3 0.012 2.6E-07 61.0 3.0 46 141-191 230-277 (348)
42 KOG2879 Predicted E3 ubiquitin 95.0 0.016 3.4E-07 57.4 2.6 49 137-192 236-287 (298)
43 KOG1812 Predicted E3 ubiquitin 95.0 0.023 5E-07 60.5 4.1 42 221-266 304-345 (384)
44 COG5432 RAD18 RING-finger-cont 94.5 0.016 3.5E-07 57.5 1.3 62 139-209 24-88 (391)
45 COG5152 Uncharacterized conser 94.4 0.0097 2.1E-07 55.8 -0.3 34 140-175 196-231 (259)
46 PF12678 zf-rbx1: RING-H2 zinc 94.0 0.029 6.3E-07 45.2 1.6 43 140-188 19-73 (73)
47 PF14570 zf-RING_4: RING/Ubox 93.6 0.023 5.1E-07 41.5 0.4 43 143-190 1-46 (48)
48 KOG1002 Nucleotide excision re 93.3 0.017 3.7E-07 61.6 -1.0 55 136-194 532-588 (791)
49 KOG4159 Predicted E3 ubiquitin 93.1 0.052 1.1E-06 57.7 2.3 47 138-193 82-130 (398)
50 KOG0006 E3 ubiquitin-protein l 93.0 0.097 2.1E-06 52.7 3.7 93 159-265 341-438 (446)
51 KOG1039 Predicted E3 ubiquitin 92.8 0.05 1.1E-06 56.6 1.6 54 136-191 157-220 (344)
52 KOG0311 Predicted E3 ubiquitin 92.7 0.0084 1.8E-07 61.3 -4.2 47 138-191 41-89 (381)
53 PF10571 UPF0547: Uncharacteri 91.9 0.074 1.6E-06 33.8 0.9 24 293-321 1-24 (26)
54 KOG4265 Predicted E3 ubiquitin 91.5 0.092 2E-06 54.1 1.6 65 121-193 268-337 (349)
55 KOG4739 Uncharacterized protei 90.7 0.14 3.1E-06 50.1 2.0 54 141-201 4-57 (233)
56 PRK00420 hypothetical protein; 90.0 3.6 7.8E-05 35.9 9.9 19 413-431 93-111 (112)
57 KOG0317 Predicted E3 ubiquitin 89.7 0.093 2E-06 52.5 -0.2 37 290-333 237-273 (293)
58 COG5243 HRD1 HRD ubiquitin lig 89.6 0.11 2.5E-06 53.4 0.4 48 138-191 285-344 (491)
59 KOG1815 Predicted E3 ubiquitin 89.3 0.34 7.3E-06 52.9 3.7 35 296-332 164-199 (444)
60 PF14447 Prok-RING_4: Prokaryo 88.6 0.24 5.1E-06 37.2 1.3 46 140-194 7-52 (55)
61 KOG1813 Predicted E3 ubiquitin 87.5 0.26 5.7E-06 49.5 1.3 43 140-191 241-285 (313)
62 KOG0297 TNF receptor-associate 87.0 0.37 8.1E-06 51.6 2.2 47 137-191 18-66 (391)
63 TIGR00570 cdk7 CDK-activating 87.0 18 0.0004 37.3 14.2 34 293-328 4-37 (309)
64 PF13240 zinc_ribbon_2: zinc-r 86.1 0.4 8.6E-06 29.5 1.1 10 294-303 1-10 (23)
65 KOG2817 Predicted E3 ubiquitin 85.9 0.98 2.1E-05 47.4 4.5 56 139-197 333-390 (394)
66 KOG1785 Tyrosine kinase negati 85.6 0.24 5.1E-06 51.5 -0.2 44 141-188 370-414 (563)
67 PF13248 zf-ribbon_3: zinc-rib 85.5 0.47 1E-05 30.1 1.2 11 293-303 3-13 (26)
68 KOG1734 Predicted RING-contain 85.1 0.58 1.3E-05 46.4 2.3 70 119-193 203-282 (328)
69 KOG1645 RING-finger-containing 85.0 0.34 7.3E-06 50.8 0.6 48 140-191 4-55 (463)
70 smart00661 RPOL9 RNA polymeras 84.7 0.64 1.4E-05 34.4 1.9 27 293-320 1-29 (52)
71 COG5220 TFB3 Cdk activating ki 84.7 0.3 6.5E-06 47.5 0.1 48 141-192 11-64 (314)
72 PF15227 zf-C3HC4_4: zinc fing 84.0 0.47 1E-05 33.8 0.8 32 295-333 1-32 (42)
73 KOG1428 Inhibitor of type V ad 83.9 0.89 1.9E-05 54.3 3.4 68 140-210 3486-3561(3738)
74 KOG0802 E3 ubiquitin ligase [P 83.8 0.23 4.9E-06 55.7 -1.3 44 140-189 291-338 (543)
75 KOG4185 Predicted E3 ubiquitin 83.7 1 2.2E-05 46.3 3.5 54 140-198 3-63 (296)
76 KOG4275 Predicted E3 ubiquitin 83.7 0.25 5.5E-06 49.4 -0.9 39 140-190 300-340 (350)
77 PHA00626 hypothetical protein 83.4 0.83 1.8E-05 34.3 1.9 30 294-324 2-36 (59)
78 COG5175 MOT2 Transcriptional r 82.6 0.31 6.6E-06 49.7 -0.8 53 140-197 14-69 (480)
79 PF14835 zf-RING_6: zf-RING of 82.2 0.66 1.4E-05 36.1 1.1 25 293-318 8-35 (65)
80 PF09297 zf-NADH-PPase: NADH p 81.3 1.7 3.8E-05 28.8 2.7 29 291-320 2-30 (32)
81 KOG2660 Locus-specific chromos 81.0 0.33 7.2E-06 49.6 -1.2 46 138-191 13-60 (331)
82 PF14952 zf-tcix: Putative tre 80.9 1.3 2.9E-05 31.5 2.1 32 286-321 5-37 (44)
83 KOG1001 Helicase-like transcri 80.9 0.53 1.2E-05 53.7 0.2 45 141-193 455-501 (674)
84 KOG4692 Predicted E3 ubiquitin 80.6 0.64 1.4E-05 47.7 0.7 50 135-193 417-468 (489)
85 KOG0823 Predicted E3 ubiquitin 80.5 0.66 1.4E-05 45.2 0.7 20 311-333 62-81 (230)
86 PF12861 zf-Apc11: Anaphase-pr 80.2 0.85 1.8E-05 37.6 1.1 33 156-191 48-81 (85)
87 PF11793 FANCL_C: FANCL C-term 79.7 0.9 2E-05 36.2 1.1 51 140-192 2-66 (70)
88 PRK14559 putative protein seri 79.6 1.1 2.4E-05 51.0 2.1 23 293-328 28-50 (645)
89 PF05883 Baculo_RING: Baculovi 79.2 0.44 9.6E-06 42.7 -0.9 32 140-171 26-65 (134)
90 KOG0825 PHD Zn-finger protein 78.2 0.43 9.4E-06 53.6 -1.5 46 141-192 124-171 (1134)
91 PLN03208 E3 ubiquitin-protein 78.1 0.97 2.1E-05 43.2 1.0 31 293-330 19-49 (193)
92 COG5222 Uncharacterized conser 77.6 0.94 2E-05 45.5 0.8 41 141-189 275-318 (427)
93 PF13719 zinc_ribbon_5: zinc-r 77.3 2.2 4.8E-05 29.4 2.3 29 224-254 3-35 (37)
94 PLN03086 PRLI-interacting fact 76.5 3.6 7.8E-05 45.9 4.9 57 178-254 406-463 (567)
95 KOG0828 Predicted E3 ubiquitin 74.3 0.76 1.6E-05 49.2 -0.9 51 138-193 569-635 (636)
96 KOG0826 Predicted E3 ubiquitin 74.0 7.2 0.00016 40.1 5.9 98 80-191 238-347 (357)
97 PF05764 YL1: YL1 nuclear prot 73.8 2.5 5.4E-05 42.2 2.6 10 5-14 24-33 (240)
98 COG5574 PEX10 RING-finger-cont 73.2 1.3 2.7E-05 44.1 0.4 34 293-333 216-250 (271)
99 PF08274 PhnA_Zn_Ribbon: PhnA 73.2 2.5 5.4E-05 27.8 1.6 27 293-321 3-29 (30)
100 KOG2807 RNA polymerase II tran 73.1 3 6.6E-05 42.6 3.0 22 242-263 342-364 (378)
101 PF13923 zf-C3HC4_2: Zinc fing 73.1 1.3 2.8E-05 30.7 0.3 32 295-332 1-32 (39)
102 KOG0827 Predicted E3 ubiquitin 72.4 0.83 1.8E-05 47.6 -1.1 54 140-196 4-60 (465)
103 PF00643 zf-B_box: B-box zinc 72.4 3.5 7.6E-05 28.9 2.4 30 292-329 3-33 (42)
104 PF00627 UBA: UBA/TS-N domain; 71.9 11 0.00023 25.8 4.7 33 79-112 3-35 (37)
105 PRK14559 putative protein seri 71.8 2.8 6E-05 47.8 2.7 12 293-304 42-53 (645)
106 PHA02926 zinc finger-like prot 70.9 2.9 6.4E-05 40.7 2.3 53 292-345 170-225 (242)
107 PF09788 Tmemb_55A: Transmembr 70.7 7 0.00015 38.8 4.9 73 138-240 63-140 (256)
108 PRK00432 30S ribosomal protein 70.6 1.6 3.5E-05 32.4 0.3 28 291-321 19-47 (50)
109 KOG0320 Predicted E3 ubiquitin 70.0 1.3 2.8E-05 41.4 -0.3 30 248-303 149-178 (187)
110 PF10446 DUF2457: Protein of u 70.0 4.1 9E-05 43.5 3.3 11 135-145 189-199 (458)
111 COG4647 AcxC Acetone carboxyla 69.7 2.6 5.6E-05 37.2 1.5 58 245-303 70-131 (165)
112 cd00021 BBOX B-Box-type zinc f 69.4 4.4 9.5E-05 27.6 2.4 26 294-327 2-28 (39)
113 PF10367 Vps39_2: Vacuolar sor 69.2 3.1 6.8E-05 35.4 1.9 31 140-170 78-108 (109)
114 PRK00398 rpoP DNA-directed RNA 69.1 3.8 8.3E-05 29.6 2.1 28 293-321 4-31 (46)
115 KOG4172 Predicted E3 ubiquitin 68.6 0.55 1.2E-05 35.1 -2.4 43 141-191 8-53 (62)
116 KOG3800 Predicted E3 ubiquitin 67.1 3.9 8.5E-05 41.2 2.4 49 142-195 2-54 (300)
117 PF04641 Rtf2: Rtf2 RING-finge 67.0 3.7 8.1E-05 41.4 2.3 67 137-210 110-180 (260)
118 PF13717 zinc_ribbon_4: zinc-r 65.8 6.1 0.00013 27.1 2.4 29 224-254 3-35 (36)
119 TIGR00622 ssl1 transcription f 65.6 6 0.00013 34.5 2.9 39 224-264 56-101 (112)
120 TIGR02098 MJ0042_CXXC MJ0042 f 65.1 3.7 7.9E-05 28.2 1.2 26 294-321 4-35 (38)
121 PF04147 Nop14: Nop14-like fam 64.5 12 0.00026 44.4 6.0 19 61-79 415-436 (840)
122 PF06677 Auto_anti-p27: Sjogre 63.3 9.7 0.00021 27.0 3.1 30 285-318 11-41 (41)
123 PF07191 zinc-ribbons_6: zinc- 62.9 5.4 0.00012 31.7 1.9 50 294-346 3-57 (70)
124 smart00744 RINGv The RING-vari 62.6 3.2 6.9E-05 30.6 0.6 40 142-184 1-47 (49)
125 TIGR03655 anti_R_Lar restricti 62.2 5.6 0.00012 29.7 1.9 28 293-321 2-36 (53)
126 PF04931 DNA_pol_phi: DNA poly 61.8 11 0.00025 44.2 5.3 13 99-111 768-780 (784)
127 KOG0825 PHD Zn-finger protein 60.7 1.4 2.9E-05 49.9 -2.4 52 140-191 96-153 (1134)
128 KOG3970 Predicted E3 ubiquitin 60.6 5.4 0.00012 38.6 1.9 48 140-191 50-104 (299)
129 PF07282 OrfB_Zn_ribbon: Putat 59.9 5.7 0.00012 31.2 1.7 28 291-319 27-54 (69)
130 KOG2906 RNA polymerase III sub 58.6 6.4 0.00014 33.2 1.7 28 293-321 2-31 (105)
131 cd00194 UBA Ubiquitin Associat 58.5 28 0.00061 23.6 4.8 35 80-115 3-37 (38)
132 PF09538 FYDLN_acid: Protein o 58.3 5.7 0.00012 34.5 1.5 27 293-321 10-36 (108)
133 COG5151 SSL1 RNA polymerase II 58.1 3.5 7.6E-05 41.8 0.2 88 161-263 307-407 (421)
134 COG5109 Uncharacterized conser 56.9 4.9 0.00011 40.9 0.9 49 139-190 335-385 (396)
135 PRK08665 ribonucleotide-diphos 56.8 6.2 0.00013 46.0 1.9 27 293-322 725-751 (752)
136 PF10168 Nup88: Nuclear pore c 56.1 2.8E+02 0.0061 32.4 15.1 45 414-472 581-625 (717)
137 PF02150 RNA_POL_M_15KD: RNA p 56.0 9 0.00019 26.1 1.9 27 224-253 2-29 (35)
138 PRK14714 DNA polymerase II lar 54.1 11 0.00024 45.5 3.4 29 223-261 667-701 (1337)
139 COG1997 RPL43A Ribosomal prote 53.7 9.7 0.00021 31.5 2.0 28 293-321 36-63 (89)
140 KOG1571 Predicted E3 ubiquitin 53.6 4.2 9.2E-05 42.3 -0.1 44 139-192 304-347 (355)
141 KOG3002 Zn finger protein [Gen 53.3 7.9 0.00017 39.9 1.8 47 137-192 45-91 (299)
142 PF13834 DUF4193: Domain of un 52.6 7 0.00015 33.2 1.1 32 137-168 67-98 (99)
143 smart00165 UBA Ubiquitin assoc 52.1 37 0.00081 22.8 4.6 32 81-113 4-35 (37)
144 smart00661 RPOL9 RNA polymeras 51.9 12 0.00026 27.4 2.2 27 225-253 2-29 (52)
145 KOG3039 Uncharacterized conser 51.8 6.1 0.00013 38.9 0.7 51 139-196 220-274 (303)
146 TIGR01384 TFS_arch transcripti 51.5 9.2 0.0002 32.7 1.7 25 293-320 1-25 (104)
147 PRK09710 lar restriction allev 50.0 13 0.00028 29.0 2.1 28 291-319 5-35 (64)
148 PRK05654 acetyl-CoA carboxylas 49.6 3.7 8.1E-05 42.1 -1.2 28 293-321 28-56 (292)
149 KOG4362 Transcriptional regula 49.4 5.3 0.00011 45.2 -0.2 52 139-196 20-73 (684)
150 PF14803 Nudix_N_2: Nudix N-te 49.1 13 0.00029 25.2 1.8 28 224-253 1-31 (34)
151 PF10446 DUF2457: Protein of u 48.8 13 0.00029 39.8 2.7 7 43-49 108-114 (458)
152 COG5432 RAD18 RING-finger-cont 48.4 7.2 0.00016 39.3 0.6 30 293-329 26-55 (391)
153 COG0266 Nei Formamidopyrimidin 47.7 14 0.0003 37.5 2.5 26 292-318 245-272 (273)
154 PRK04023 DNA polymerase II lar 47.7 14 0.0003 43.7 2.8 33 220-262 623-661 (1121)
155 PHA02929 N1R/p28-like protein; 47.4 10 0.00022 37.8 1.5 40 292-333 174-216 (238)
156 TIGR00686 phnA alkylphosphonat 46.8 15 0.00033 31.6 2.3 26 293-320 3-28 (109)
157 KOG0943 Predicted ubiquitin-pr 46.8 13 0.00029 44.3 2.4 16 452-467 2419-2434(3015)
158 COG1645 Uncharacterized Zn-fin 46.8 12 0.00026 33.5 1.7 23 293-326 29-51 (131)
159 PHA03096 p28-like protein; Pro 46.7 4.6 0.0001 41.3 -1.1 30 141-170 179-214 (284)
160 PF06827 zf-FPG_IleRS: Zinc fi 46.6 15 0.00032 23.9 1.7 25 293-318 2-28 (30)
161 KOG2177 Predicted E3 ubiquitin 46.2 7.8 0.00017 38.8 0.5 25 294-326 88-112 (386)
162 COG5236 Uncharacterized conser 45.7 9.3 0.0002 39.4 0.9 49 137-191 58-107 (493)
163 TIGR00515 accD acetyl-CoA carb 45.4 4.7 0.0001 41.2 -1.2 28 293-321 27-55 (285)
164 KOG3579 Predicted E3 ubiquitin 45.1 13 0.00029 37.3 1.9 49 139-189 267-322 (352)
165 COG3809 Uncharacterized protei 44.9 13 0.00028 30.0 1.4 35 293-334 2-36 (88)
166 KOG3161 Predicted E3 ubiquitin 44.8 4.7 0.0001 44.8 -1.4 31 140-170 11-43 (861)
167 PF09889 DUF2116: Uncharacteri 44.5 5.4 0.00012 30.7 -0.7 24 293-329 4-28 (59)
168 PF14569 zf-UDP: Zinc-binding 44.3 11 0.00024 30.5 0.9 48 138-191 7-61 (80)
169 PF12861 zf-Apc11: Anaphase-pr 44.1 14 0.00031 30.6 1.6 36 293-333 33-68 (85)
170 COG1594 RPB9 DNA-directed RNA 43.4 19 0.00041 31.5 2.4 29 292-321 2-32 (113)
171 PRK14892 putative transcriptio 43.4 17 0.00038 31.0 2.1 27 293-320 22-51 (99)
172 PF07975 C1_4: TFIIH C1-like d 43.4 11 0.00025 28.0 0.9 22 244-265 20-42 (51)
173 CHL00174 accD acetyl-CoA carbo 43.2 5.1 0.00011 41.1 -1.4 28 293-321 39-67 (296)
174 COG1198 PriA Primosomal protei 42.9 16 0.00034 42.3 2.3 35 293-328 445-484 (730)
175 COG2888 Predicted Zn-ribbon RN 42.3 12 0.00025 28.7 0.8 7 293-299 28-34 (61)
176 KOG4739 Uncharacterized protei 42.3 3E+02 0.0066 27.3 10.7 23 306-329 21-47 (233)
177 COG1998 RPS31 Ribosomal protei 42.1 17 0.00037 26.8 1.5 26 293-319 20-45 (51)
178 PRK14811 formamidopyrimidine-D 42.0 19 0.0004 36.6 2.5 27 292-319 235-263 (269)
179 PF12773 DZR: Double zinc ribb 41.5 13 0.00028 27.1 0.9 11 293-303 13-23 (50)
180 PF01396 zf-C4_Topoisom: Topoi 41.5 28 0.0006 24.3 2.5 21 293-314 2-25 (39)
181 PRK14892 putative transcriptio 41.4 56 0.0012 27.9 4.9 55 220-279 18-74 (99)
182 PRK12495 hypothetical protein; 41.1 19 0.00041 35.1 2.2 24 292-318 42-65 (226)
183 PF03884 DUF329: Domain of unk 40.9 5.5 0.00012 30.4 -1.1 38 292-333 2-40 (57)
184 PRK01103 formamidopyrimidine/5 40.9 21 0.00045 36.3 2.6 27 292-319 245-273 (274)
185 PF03119 DNA_ligase_ZBD: NAD-d 40.8 26 0.00057 22.6 2.1 21 294-314 1-21 (28)
186 smart00336 BBOX B-Box-type zin 40.7 23 0.00049 24.4 2.1 28 293-328 4-32 (42)
187 PRK10220 hypothetical protein; 40.3 23 0.0005 30.6 2.3 27 292-320 3-29 (111)
188 PRK11827 hypothetical protein; 40.0 23 0.0005 27.3 2.1 26 293-319 9-34 (60)
189 TIGR00577 fpg formamidopyrimid 39.7 22 0.00048 36.1 2.6 25 293-318 246-272 (272)
190 PF02845 CUE: CUE domain; Int 39.2 86 0.0019 21.9 4.9 37 79-115 2-39 (42)
191 PRK10445 endonuclease VIII; Pr 38.7 23 0.00051 35.8 2.6 26 292-318 235-262 (263)
192 PRK14810 formamidopyrimidine-D 38.5 23 0.0005 36.0 2.5 26 292-318 244-271 (272)
193 TIGR00599 rad18 DNA repair pro 38.1 13 0.00027 39.9 0.6 33 293-332 27-59 (397)
194 PRK13945 formamidopyrimidine-D 37.6 24 0.00053 36.0 2.6 26 292-318 254-281 (282)
195 KOG2164 Predicted E3 ubiquitin 37.2 14 0.00031 40.2 0.8 28 293-327 187-214 (513)
196 smart00804 TAP_C C-terminal do 37.0 1E+02 0.0022 24.0 5.3 40 75-114 9-48 (63)
197 PF05715 zf-piccolo: Piccolo Z 36.6 14 0.00031 28.2 0.5 40 293-333 3-44 (61)
198 TIGR02300 FYDLN_acid conserved 36.5 20 0.00044 31.8 1.5 26 293-320 10-35 (129)
199 PF14445 Prok-RING_2: Prokaryo 36.3 5.2 0.00011 29.4 -1.8 32 139-170 6-38 (57)
200 KOG2114 Vacuolar assembly/sort 36.1 20 0.00044 41.4 1.8 101 77-189 758-880 (933)
201 COG0777 AccD Acetyl-CoA carbox 35.6 11 0.00024 37.9 -0.3 28 293-321 29-57 (294)
202 KOG2932 E3 ubiquitin ligase in 35.4 8.3 0.00018 39.3 -1.2 53 220-309 87-140 (389)
203 PTZ00007 (NAP-L) nucleosome as 34.7 46 0.00099 34.9 4.0 13 7-19 273-285 (337)
204 PF09726 Macoilin: Transmembra 34.3 5.9E+02 0.013 29.7 13.2 72 412-500 587-658 (697)
205 KOG1952 Transcription factor N 34.3 27 0.00059 40.4 2.4 49 138-188 189-243 (950)
206 PF09943 DUF2175: Uncharacteri 34.1 74 0.0016 27.2 4.4 25 447-471 75-99 (101)
207 PF13453 zf-TFIIB: Transcripti 34.0 24 0.00051 24.8 1.3 31 294-331 1-31 (41)
208 PF03943 TAP_C: TAP C-terminal 33.9 46 0.00099 24.7 2.8 36 80-115 2-37 (51)
209 KOG1941 Acetylcholine receptor 33.9 6.8 0.00015 41.1 -2.2 47 139-189 364-413 (518)
210 PF03615 GCM: GCM motif protei 33.9 40 0.00088 30.1 2.9 37 263-320 68-106 (143)
211 PF08271 TF_Zn_Ribbon: TFIIB z 33.0 47 0.001 23.5 2.7 21 294-314 2-23 (43)
212 KOG2906 RNA polymerase III sub 33.0 34 0.00074 29.0 2.2 29 224-254 2-31 (105)
213 PF09862 DUF2089: Protein of u 32.9 2.3E+02 0.0049 24.9 7.3 9 295-303 1-9 (113)
214 PRK11546 zraP zinc resistance 32.8 3.9E+02 0.0085 24.5 10.0 55 446-500 46-104 (143)
215 PF08792 A2L_zn_ribbon: A2L zi 32.6 35 0.00077 22.9 1.8 27 292-319 3-29 (33)
216 PF14149 YhfH: YhfH-like prote 32.5 3.9 8.4E-05 28.2 -2.8 25 292-317 13-37 (37)
217 PRK14714 DNA polymerase II lar 32.5 22 0.00048 43.1 1.4 30 293-329 668-702 (1337)
218 PHA02664 hypothetical protein; 32.2 1.1E+02 0.0024 31.5 6.0 10 80-89 523-532 (534)
219 PF12325 TMF_TATA_bd: TATA ele 32.2 3.6E+02 0.0078 23.9 10.5 24 485-508 96-119 (120)
220 PRK09521 exosome complex RNA-b 31.8 33 0.00071 32.8 2.3 25 294-320 151-175 (189)
221 smart00659 RPOLCX RNA polymera 31.6 38 0.00083 24.3 2.0 24 294-319 4-27 (44)
222 TIGR01206 lysW lysine biosynth 31.5 50 0.0011 24.9 2.7 28 225-254 4-32 (54)
223 PF00098 zf-CCHC: Zinc knuckle 30.7 32 0.00069 19.7 1.2 16 254-269 2-17 (18)
224 KOG2932 E3 ubiquitin ligase in 30.4 27 0.00058 35.7 1.4 29 293-328 91-120 (389)
225 COG5219 Uncharacterized conser 30.4 7.2 0.00016 45.3 -2.8 51 138-192 1467-1523(1525)
226 COG2816 NPY1 NTP pyrophosphohy 30.1 40 0.00087 34.3 2.6 36 284-321 104-139 (279)
227 PF01599 Ribosomal_S27: Riboso 29.9 34 0.00074 25.0 1.5 26 293-319 19-46 (47)
228 PF05290 Baculo_IE-1: Baculovi 29.9 18 0.00039 32.4 0.1 51 137-191 77-131 (140)
229 PF01428 zf-AN1: AN1-like Zinc 29.7 33 0.00072 24.3 1.4 31 226-263 1-33 (43)
230 PRK09710 lar restriction allev 29.4 57 0.0012 25.5 2.7 34 222-256 5-39 (64)
231 KOG2034 Vacuolar sorting prote 29.3 19 0.00042 41.8 0.2 32 139-170 816-847 (911)
232 PF07417 Crl: Transcriptional 29.2 85 0.0018 27.9 4.1 47 430-476 64-110 (125)
233 KOG4460 Nuclear pore complex, 29.2 7E+02 0.015 28.0 11.7 15 506-520 668-682 (741)
234 PF14446 Prok-RING_1: Prokaryo 28.6 31 0.00068 26.0 1.1 31 140-170 5-37 (54)
235 PRK12286 rpmF 50S ribosomal pr 28.5 36 0.00078 26.0 1.5 23 291-319 26-48 (57)
236 KOG2789 Putative Zn-finger pro 28.2 33 0.00071 36.3 1.6 34 137-170 71-104 (482)
237 PHA02325 hypothetical protein 28.2 27 0.00058 27.1 0.8 13 291-303 2-14 (72)
238 KOG3799 Rab3 effector RIM1 and 28.1 26 0.00056 31.3 0.8 37 294-333 67-103 (169)
239 PF06044 DRP: Dam-replacing fa 28.1 41 0.0009 33.3 2.2 36 284-321 24-63 (254)
240 PLN02189 cellulose synthase 28.0 35 0.00076 40.8 2.0 47 139-191 33-86 (1040)
241 PF01363 FYVE: FYVE zinc finge 27.9 42 0.0009 26.1 1.9 34 137-170 6-41 (69)
242 cd07620 BAR_SH3BP1 The Bin/Amp 27.8 6.4E+02 0.014 25.4 11.2 112 412-531 118-249 (257)
243 smart00546 CUE Domain that may 27.6 1.9E+02 0.0041 20.2 5.1 38 79-116 3-41 (43)
244 KOG1991 Nuclear transport rece 27.5 1E+02 0.0022 36.6 5.5 33 69-104 955-987 (1010)
245 PF01783 Ribosomal_L32p: Ribos 27.3 27 0.00058 26.5 0.6 22 291-318 25-46 (56)
246 COG2824 PhnA Uncharacterized Z 27.0 45 0.00097 28.7 1.9 24 293-319 4-28 (112)
247 PRK01343 zinc-binding protein; 26.4 27 0.00058 26.7 0.5 12 292-303 9-20 (57)
248 PRK08115 ribonucleotide-diphos 26.4 34 0.00073 40.3 1.5 25 293-320 828-853 (858)
249 TIGR02159 PA_CoA_Oxy4 phenylac 26.3 42 0.00091 30.8 1.8 93 73-170 39-138 (146)
250 TIGR01031 rpmF_bact ribosomal 26.2 40 0.00087 25.5 1.4 23 291-319 25-47 (55)
251 PF03115 Astro_capsid: Astrovi 26.0 23 0.00049 41.3 0.0 15 90-104 721-736 (787)
252 COG1096 Predicted RNA-binding 25.8 45 0.00097 31.8 1.9 24 293-319 150-173 (188)
253 PF14354 Lar_restr_allev: Rest 25.5 58 0.0013 24.6 2.3 29 222-252 2-37 (61)
254 TIGR02443 conserved hypothetic 25.3 63 0.0014 24.8 2.3 27 293-320 10-40 (59)
255 PF03604 DNA_RNApol_7kD: DNA d 25.2 41 0.00089 22.5 1.1 9 295-303 3-11 (32)
256 PLN02638 cellulose synthase A 25.1 53 0.0012 39.5 2.8 47 139-191 16-69 (1079)
257 COG4640 Predicted membrane pro 24.9 3E+02 0.0065 29.5 7.8 23 293-321 2-25 (465)
258 COG5220 TFB3 Cdk activating ki 24.4 39 0.00085 33.3 1.3 54 179-236 10-64 (314)
259 KOG2041 WD40 repeat protein [G 24.4 84 0.0018 36.0 3.9 33 187-219 1076-1108(1189)
260 PF02318 FYVE_2: FYVE-type zin 24.4 44 0.00095 29.3 1.5 36 291-328 53-88 (118)
261 TIGR00595 priA primosomal prot 24.1 50 0.0011 36.7 2.3 35 293-328 223-262 (505)
262 PF07058 Myosin_HC-like: Myosi 23.9 8.2E+02 0.018 25.3 14.0 22 501-522 144-165 (351)
263 PLN02436 cellulose synthase A 23.9 53 0.0012 39.4 2.5 47 139-191 35-88 (1094)
264 KOG3183 Predicted Zn-finger pr 23.8 16 0.00035 35.9 -1.4 39 224-269 99-138 (250)
265 PF14353 CpXC: CpXC protein 23.8 49 0.0011 29.3 1.8 46 180-237 2-50 (128)
266 PRK00418 DNA gyrase inhibitor; 23.7 34 0.00075 26.6 0.6 12 292-303 6-17 (62)
267 PF10122 Mu-like_Com: Mu-like 23.7 33 0.00071 25.5 0.5 26 293-319 5-32 (51)
268 KOG0219 Mismatch repair ATPase 23.3 1.2E+03 0.026 27.6 12.7 29 484-512 458-486 (902)
269 COG0021 TktA Transketolase [Ca 23.3 3.9E+02 0.0083 30.6 8.8 98 422-524 270-379 (663)
270 PLN03184 chloroplast Hsp70; Pr 23.0 1.2E+03 0.025 27.0 13.2 19 68-86 146-164 (673)
271 PF05129 Elf1: Transcription e 22.9 38 0.00082 27.8 0.8 28 293-321 23-56 (81)
272 PLN02189 cellulose synthase 22.7 63 0.0014 38.7 2.8 60 224-311 35-95 (1040)
273 KOG2662 Magnesium transporters 22.5 3.8E+02 0.0083 28.8 8.2 42 485-526 220-263 (414)
274 PRK04023 DNA polymerase II lar 22.5 38 0.00082 40.2 0.9 30 291-327 625-659 (1121)
275 PF12760 Zn_Tnp_IS1595: Transp 22.4 1.3E+02 0.0027 21.6 3.4 28 291-319 17-45 (46)
276 KOG0956 PHD finger protein AF1 22.4 1.1E+02 0.0023 35.0 4.2 34 222-259 21-55 (900)
277 PLN02638 cellulose synthase A 22.3 58 0.0013 39.1 2.4 55 231-311 23-78 (1079)
278 KOG1940 Zn-finger protein [Gen 22.0 41 0.00089 34.2 1.0 46 137-189 155-204 (276)
279 PF09526 DUF2387: Probable met 21.9 75 0.0016 25.4 2.3 27 293-320 9-39 (71)
280 COG1594 RPB9 DNA-directed RNA 21.9 76 0.0017 27.8 2.5 30 223-254 2-32 (113)
281 PTZ00009 heat shock 70 kDa pro 21.8 1.2E+03 0.027 26.6 14.0 33 486-518 590-622 (653)
282 COG3024 Uncharacterized protei 21.8 43 0.00093 26.1 0.8 13 292-304 7-19 (65)
283 COG1315 Uncharacterized conser 21.7 5.6E+02 0.012 28.5 9.3 38 367-404 408-445 (543)
284 cd07621 BAR_SNX5_6 The Bin/Amp 20.9 8.1E+02 0.017 24.1 15.1 60 452-516 156-215 (219)
285 PF03854 zf-P11: P-11 zinc fin 20.7 25 0.00053 25.8 -0.6 44 141-193 3-47 (50)
286 COG3813 Uncharacterized protei 20.6 44 0.00095 26.6 0.7 42 142-191 7-51 (84)
287 PF06705 SF-assemblin: SF-asse 20.4 8.4E+02 0.018 24.1 16.1 16 370-385 13-28 (247)
288 PRK00241 nudC NADH pyrophospha 20.4 70 0.0015 32.2 2.3 34 285-320 93-126 (256)
289 PF08580 KAR9: Yeast cortical 20.3 1.4E+03 0.03 26.6 13.7 22 448-469 270-291 (683)
290 KOG2879 Predicted E3 ubiquitin 20.3 42 0.00091 33.8 0.6 31 292-328 239-269 (298)
291 PF06056 Terminase_5: Putative 20.2 1.3E+02 0.0028 22.9 3.2 34 79-112 13-46 (58)
292 KOG4684 Uncharacterized conser 20.1 95 0.0021 30.1 2.9 70 140-239 80-154 (275)
293 PF07754 DUF1610: Domain of un 20.1 78 0.0017 19.8 1.5 7 293-299 17-23 (24)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-71 Score=597.56 Aligned_cols=432 Identities=47% Similarity=0.905 Sum_probs=392.0
Q ss_pred EecHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhhcChHHHHHHcCCCCCCccccCCCCcccccccc
Q 008581 68 VLREADIKCQQEDDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWFADEDAVRKSVGFLDKPVVEFSNARELTCGICF 147 (561)
Q Consensus 68 vlt~~~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~C~IC~ 147 (561)
|++.++|...|.++|..|+++|++++.+|++||.+|.|+.+++++.|+.+++.++..+|+...+ .......|.||+
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~----~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWP----KKKGDVQCGICV 77 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccC----CCCccccCCccc
Confidence 6889999999999999999999999999999999999999999999999999999999986653 345578999999
Q ss_pred ccccCCCeeeccCCCccccccce------eccCCcccccccCCCCCCCcchhhHHhhhCCh-HHHHHHHHHHHHHHHhcC
Q 008581 148 DTYSCDKVVSAACGHPFCRACWR------VNDGPGCLMLRCPDPSCCAAVGQDMIDMLASD-EDKKKYSRYLLRSYVEDN 220 (561)
Q Consensus 148 e~~~~~~~~~l~CgH~fC~~C~~------i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~-e~~~ky~~~l~~~~v~~~ 220 (561)
+.++. .+..+.|||.||..||. |..+.... |+||..+|...+..+.|..++++ +..++|.+++.++|++.+
T Consensus 78 ~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~-i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~ 155 (444)
T KOG1815|consen 78 ESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK-IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-hhhhcCCCcHHHHHHHHHHhhheeecccccc-ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 98865 67888999999999999 66665433 99999999999999999999988 599999999999999999
Q ss_pred CCceecCCCCCCCeeecccCCCCceeEecCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCCCc
Q 008581 221 RKTKWCPAPGCEHAIDFAAGSGNFDVSCLCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKCKR 300 (561)
Q Consensus 221 ~~~~~CP~~~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C~~ 300 (561)
..++|||+|+|++++.+. ......|.|.|++.|||.|+.+||.|.+|.....|+.+..+++++.+||..|+++||+|..
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~ 234 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKV 234 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCccc
Confidence 999999999999999875 4556789999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecCCCCceEeCCC--CcchhhhhhhcCccCCCCCCCCcccCCcchhhhhcCCchHHHHHHHHHHHHHhhhHHHHHHH
Q 008581 301 PIEKNQGCMHMTCSPP--CKFEFCWLCLGAWSDHGERTGGFYACNRYETAKQQGDYDETERRREMAKNSLEKYTHYYERW 378 (561)
Q Consensus 301 ~IEK~~GCnhm~C~~~--C~~~FCw~C~~~w~~h~~~~g~~y~C~~~~~~~~~~~~~~~~~~~~~~~~~l~ry~~y~~r~ 378 (561)
+|||++|||||+|. . |++.|||+|++.|..|+..+ +|.||+|...+.. . .+++++..|.||.|||+||
T Consensus 235 ~iek~~gc~~~~~~-~~~c~~~FCw~Cl~~~~~h~~~~--~~~c~~~~~~~~~------~-~~~~a~~~l~r~~~~~~~~ 304 (444)
T KOG1815|consen 235 PIEKDGGCNHMTCK-SASCKHEFCWVCLASLSDHGSST--GYSCNRYVDGKSK------S-ARSKARRSLKRYTHYYNRW 304 (444)
T ss_pred chhccCCccccccc-cCCcCCeeceeeecccccccccc--eeeeeeeechhhh------h-HHHHHHHHHHHHHHHHhhH
Confidence 99999999999998 6 99999999999999999754 8999999764421 1 4678899999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHhhcccceecccCccchhhhhHHHHHHHH
Q 008581 379 ASNQSSRQKALADLHQMQTVHLEKLSDIQCTPESQLKFIIDAWLQIVECRRVLKWTYAYGYYLPEHEHAKRQFFEYLQGE 458 (561)
Q Consensus 379 ~~h~~s~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~fl~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~ 458 (561)
++|+.+++++...+......+..++......++++++|+.+++.+|.++|++|+|||+|+||+. ...++++||++|.+
T Consensus 305 ~~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~--~~~~~~~fe~~q~~ 382 (444)
T KOG1815|consen 305 MEHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLS--ENNKRNLFEDNQTD 382 (444)
T ss_pred HhhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhc--ccchhhhhHHHHHH
Confidence 9999999998877777777777777777677789999999999999999999999999999997 44567999999999
Q ss_pred HHHhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccc
Q 008581 459 AESGLERLHQCAEKELLQFLNDESQSKEFNDFRTKLAGLTSVTKNYFENLVRALENGLADVDSHA 523 (561)
Q Consensus 459 ~e~~~e~L~~~le~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~ 523 (561)
|+..+|.|+..+|.++. +.+...+..+|.++.++|.++++|+++++..+++||.++.+..
T Consensus 383 ~~~~~e~ls~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 442 (444)
T KOG1815|consen 383 LESAVEPLSSCLEESLK-----DISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLEDVGSEA 442 (444)
T ss_pred HhhhhhhhHHHhccccc-----cCCcccHHHHHhhccccchhhhhHHHHHHHHHHhccccccccc
Confidence 99999999999998776 4555789999999999999999999999999999999987643
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.9e-33 Score=294.99 Aligned_cols=218 Identities=27% Similarity=0.634 Sum_probs=179.8
Q ss_pred CccccccccccccCC-Cee-eccCCCccccccce--ecc-CCcccccccCCCCCCCcchhhHHhhhCChHHHHHHHHHHH
Q 008581 139 RELTCGICFDTYSCD-KVV-SAACGHPFCRACWR--VND-GPGCLMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSRYLL 213 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~-~~~-~l~CgH~fC~~C~~--i~~-g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l~ 213 (561)
...+|.||+...+.. .++ ...|+|.||.+||+ |.. +.....++||..+|...++.+....++++.+.+.|.+++.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~ 224 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLK 224 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHH
Confidence 367899999544332 444 46799999999999 321 2223589999999999999999999999999999999999
Q ss_pred HHHHhcCCCceecCCCCCCCeeecccC---CCCceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHH
Q 008581 214 RSYVEDNRKTKWCPAPGCEHAIDFAAG---SGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWIL 289 (561)
Q Consensus 214 ~~~v~~~~~~~~CP~~~C~~~i~~~~~---~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~ 289 (561)
+.++...... +||.|+|...+..... .......| .|+..||..|+.+||.+.+|.++++|......+....+|+.
T Consensus 225 e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la 303 (384)
T KOG1812|consen 225 EEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA 303 (384)
T ss_pred HHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH
Confidence 9999988877 9999999877654322 12233468 99999999999999999999999999877677778888888
Q ss_pred hcCCCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCCCCCCCcccCCcchhhhhcCCchHHHHHHHHHHHHHh
Q 008581 290 ANSKPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHGERTGGFYACNRYETAKQQGDYDETERRREMAKNSLE 369 (561)
Q Consensus 290 ~ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~~~~g~~y~C~~~~~~~~~~~~~~~~~~~~~~~~~l~ 369 (561)
.+++.||+|+..|++++|||||+|+ ||++|||.|+++|..|+. .+|.|.++...
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~Cr--C~~~fcy~C~~~~~~~~~---~~~~~~r~~~~--------------------- 357 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCR--CGHQFCYMCGGDWKTHNG---ECYECCRYKES--------------------- 357 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEee--ccccchhhcCcchhhCCc---cccCccccccc---------------------
Confidence 8999999999999999999999998 999999999999998874 56777776421
Q ss_pred hhHHHHHHHhhhHHHH
Q 008581 370 KYTHYYERWASNQSSR 385 (561)
Q Consensus 370 ry~~y~~r~~~h~~s~ 385 (561)
++||.++.+|..+.
T Consensus 358 --~~~~~~~~~~~~~~ 371 (384)
T KOG1812|consen 358 --THYFEDDENHDKSI 371 (384)
T ss_pred --cccccccccccccc
Confidence 56777777776554
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.1e-32 Score=274.55 Aligned_cols=190 Identities=28% Similarity=0.683 Sum_probs=162.7
Q ss_pred CCCccccccccccccC-CCeeeccCCCccccccce------eccCCcccccccCCCCCCCcchhhHHhhhCChHHHHHHH
Q 008581 137 NARELTCGICFDTYSC-DKVVSAACGHPFCRACWR------VNDGPGCLMLRCPDPSCCAAVGQDMIDMLASDEDKKKYS 209 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~------i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~ 209 (561)
..+.+.|.|||+.... ..++.+||+|.||+.|++ |.+|. ...++||+++|+...++..++.++..+++++|.
T Consensus 181 ~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~-v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQ-VSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcce-eeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 3557899999998765 567889999999999999 66664 468999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCceecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCchhHH--------HHH-----
Q 008581 210 RYLLRSYVEDNRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVA--------KWI----- 275 (561)
Q Consensus 210 ~~l~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~--------~~~----- 275 (561)
++++++.++...++++||++.|..++... .+..-+.| .|.++||+.|+..||...+|.... .|.
T Consensus 260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~d--~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRACCQLPVKQD--PGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCccccC--chhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 99999999999999999999999988433 45566789 999999999999999999997531 221
Q ss_pred --------------HHhHhhhHhHHHHHhcCCCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCcc
Q 008581 276 --------------LKNCAESENMNWILANSKPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWS 330 (561)
Q Consensus 276 --------------~k~~~~~~~~~wi~~ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~ 330 (561)
+....+..+.+|+..|.|+||+|+++|||++|||||+|. .|++.|||+|.....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~-~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT-KCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec-cccccceeehhhhcC
Confidence 111233446689999999999999999999999999999 899999999987544
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.4e-23 Score=204.46 Aligned_cols=189 Identities=33% Similarity=0.741 Sum_probs=141.3
Q ss_pred CCCCccccccccccccCCCeeeccCC--Cccccccce------eccC-----C-cccccccCCCCCCCcchhh-HHhhhC
Q 008581 136 SNARELTCGICFDTYSCDKVVSAACG--HPFCRACWR------VNDG-----P-GCLMLRCPDPSCCAAVGQD-MIDMLA 200 (561)
Q Consensus 136 ~~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~------i~~g-----~-~~~~i~CP~~~C~~~v~~~-~i~~ll 200 (561)
.+....+|-.|-+.- +.+..++|. |..|.+|++ +++. + --..+.||. +|...+-.+ .-.+++
T Consensus 217 ~N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 217 TNSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred cccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 456778999998764 445567898 999999999 3221 1 124688986 887765333 334688
Q ss_pred ChHHHHHHHHHHHHHHHhcCCCceecCCCCCCCeeecccCCCCceeEe--cCCcccccccCcccCCCCCchhHHHH----
Q 008581 201 SDEDKKKYSRYLLRSYVEDNRKTKWCPAPGCEHAIDFAAGSGNFDVSC--LCSYNFCWNCTEEAHRPVDCGTVAKW---- 274 (561)
Q Consensus 201 ~~e~~~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~~v~C--~C~~~fC~~C~~~~H~p~~C~~~~~~---- 274 (561)
..+.+.+|+++..+.+|.... -+.||+|+|+..+...+ ....|+| .||+.||..|++.+|.+. |.....-
T Consensus 294 g~e~Y~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~t~ 369 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASGTT 369 (446)
T ss_pred chhHHHHHHHhhhhhheeecC-CEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhcccc-ceeeecccccc
Confidence 999999999999999987766 57999999998887664 4567899 599999999999999763 3311000
Q ss_pred -----HHHhHh-----hhHhHHHHHhcCCCCCCCCcceeecCCCCceEeC-CCCcchhhhhhhcCccC
Q 008581 275 -----ILKNCA-----ESENMNWILANSKPCPKCKRPIEKNQGCMHMTCS-PPCKFEFCWLCLGAWSD 331 (561)
Q Consensus 275 -----~~k~~~-----~~~~~~wi~~ntK~CP~C~~~IEK~~GCnhm~C~-~~C~~~FCw~C~~~w~~ 331 (561)
+..+.+ +..+..-|...||+||+|+.|.||||||+||.|. |.||.+|||.|+.+|..
T Consensus 370 tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 370 TCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 001111 1223334778899999999999999999999999 36999999999999973
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.27 E-value=7.2e-12 Score=98.34 Aligned_cols=63 Identities=48% Similarity=1.034 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHhcCCCceecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCc
Q 008581 206 KKYSRYLLRSYVEDNRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDC 268 (561)
Q Consensus 206 ~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 268 (561)
++|.+++++++|+.+++++|||+|+|+.++......+...|.| .|++.||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4789999999999989999999999999998763346678999 99999999999999999987
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=99.13 E-value=9.9e-12 Score=97.51 Aligned_cols=63 Identities=38% Similarity=0.964 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHhcCCCceecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCc
Q 008581 206 KKYSRYLLRSYVEDNRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDC 268 (561)
Q Consensus 206 ~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 268 (561)
++|.+++++.+++.++.++|||+|+|+.++..........|+| .|++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 4788889999998888999999999999998775444334899 69999999999999999887
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.56 E-value=2e-08 Score=71.84 Aligned_cols=39 Identities=38% Similarity=0.986 Sum_probs=27.8
Q ss_pred cccccccccCCCeeeccCCCccccccce--eccCCcccccccCC
Q 008581 143 CGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPD 184 (561)
Q Consensus 143 C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~ 184 (561)
|+||++.+ .+|++++|||.||..|+. +.... ...+.||.
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~-~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPS-GSGFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSS-SST---SS
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccC-CcCCCCcC
Confidence 89999998 899999999999999999 44332 22488997
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=1e-06 Score=81.03 Aligned_cols=54 Identities=30% Similarity=0.754 Sum_probs=42.5
Q ss_pred CCCCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHH
Q 008581 136 SNARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 136 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
.+.+.+.||||++.+....+++..|||.||..|++ +.. ...||. |+..|+...+
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~-----~~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN-----TNKCPT--CRKKITHKQF 182 (187)
T ss_pred ccccccCCCceecchhhccccccccchhHHHHHHHHHHHh-----CCCCCC--cccccchhhh
Confidence 34556899999999987888899999999999999 433 457998 6666655444
No 9
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=98.02 E-value=2.1e-05 Score=81.08 Aligned_cols=78 Identities=21% Similarity=0.405 Sum_probs=46.6
Q ss_pred CceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCCCcceeecCCCCc-eEeCCCCcch
Q 008581 243 NFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKCKRPIEKNQGCMH-MTCSPPCKFE 320 (561)
Q Consensus 243 ~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C~~~IEK~~GCnh-m~C~~~C~~~ 320 (561)
...|.| .|...+|--|...-|.|-.--..+.++..+..- -+...-....-.|-.+ .|=|| |+|. .|+.-
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~gr-vs~~~s~r~~~~ct~h-------~~e~~smyc~-~ck~p 244 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGR-VSRRLSPRKVSTCTDH-------ELENHSMYCV-QCKMP 244 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCc-eeeccchhhhhhccCC-------CCCCceEEEE-ecCCh
Confidence 356789 999999999999889876444444433322110 0000000011234332 22233 9999 89999
Q ss_pred hhhhhhcCc
Q 008581 321 FCWLCLGAW 329 (561)
Q Consensus 321 FCw~C~~~w 329 (561)
.||.|+.+-
T Consensus 245 vc~~clee~ 253 (699)
T KOG4367|consen 245 VCYQCLEEG 253 (699)
T ss_pred HHHHHHHhh
Confidence 999999764
No 10
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.97 E-value=7.3e-06 Score=63.98 Aligned_cols=39 Identities=38% Similarity=1.031 Sum_probs=34.9
Q ss_pred cCCCCC--CCCcceeecC--CCCceEeCCCCcchhhhhhhcCcc
Q 008581 291 NSKPCP--KCKRPIEKNQ--GCMHMTCSPPCKFEFCWLCLGAWS 330 (561)
Q Consensus 291 ntK~CP--~C~~~IEK~~--GCnhm~C~~~C~~~FCw~C~~~w~ 330 (561)
+.+.|| +|+..|+... |..+|+|. .|++.|||.|+.+|+
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~-~C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCP-KCGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECC-CCCCeECCCCCCcCC
Confidence 358899 9999999965 99999996 699999999999984
No 11
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.95 E-value=1.3e-06 Score=62.64 Aligned_cols=39 Identities=31% Similarity=0.908 Sum_probs=19.9
Q ss_pred cccccccccC--CCeeeccCCCccccccce-e-ccCCcccccccC
Q 008581 143 CGICFDTYSC--DKVVSAACGHPFCRACWR-V-NDGPGCLMLRCP 183 (561)
Q Consensus 143 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~-i-~~g~~~~~i~CP 183 (561)
|+||.+ +.. ..++.|+|||.||.+|+. + ..+. ...++||
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 622 237889999999999999 3 3221 2378888
No 12
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=97.92 E-value=2.7e-06 Score=66.45 Aligned_cols=38 Identities=42% Similarity=1.073 Sum_probs=29.6
Q ss_pred CCCCCC--CCcceeecCCCCc--eEeCCCCcchhhhhhhcCcc
Q 008581 292 SKPCPK--CKRPIEKNQGCMH--MTCSPPCKFEFCWLCLGAWS 330 (561)
Q Consensus 292 tK~CP~--C~~~IEK~~GCnh--m~C~~~C~~~FCw~C~~~w~ 330 (561)
.+.||+ |...|++..|+++ |+|. .|++.|||.|+.+|+
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~-~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCP-SCGTEFCFKCGEPWH 59 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTT-SCCSEECSSSTSESC
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECC-CCCCcCccccCcccC
Confidence 479988 9999999999999 9998 899999999999993
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.84 E-value=4.7e-06 Score=78.72 Aligned_cols=58 Identities=26% Similarity=0.596 Sum_probs=43.6
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce-eccC------------CcccccccCCCCCCCcchhhHHhhh
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDG------------PGCLMLRCPDPSCCAAVGQDMIDML 199 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g------------~~~~~i~CP~~~C~~~v~~~~i~~l 199 (561)
.+.+.|+||++.+ .+++.++|||.||..|+. |... ......+||. |+..+....+..+
T Consensus 16 ~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPi 86 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPI 86 (193)
T ss_pred CCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEe
Confidence 4578999999976 788889999999999998 4210 0113578998 9999877655443
No 14
>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=97.82 E-value=5.4e-06 Score=58.29 Aligned_cols=36 Identities=36% Similarity=0.950 Sum_probs=26.7
Q ss_pred cccccccccCCCe-eeccCCCccccccce-eccCCcccccccCC
Q 008581 143 CGICFDTYSCDKV-VSAACGHPFCRACWR-VNDGPGCLMLRCPD 184 (561)
Q Consensus 143 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~ 184 (561)
|+||++.+ .++ +.++|||.||..||. +.... .+||.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~----~~CP~ 38 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN----PKCPV 38 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT----SB-TT
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc----CCCcC
Confidence 89999987 556 679999999999999 33222 57886
No 15
>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=97.79 E-value=6.4e-06 Score=58.46 Aligned_cols=37 Identities=38% Similarity=1.072 Sum_probs=29.6
Q ss_pred cccccccccCCCee-eccCCCccccccce--eccCCcccccccCC
Q 008581 143 CGICFDTYSCDKVV-SAACGHPFCRACWR--VNDGPGCLMLRCPD 184 (561)
Q Consensus 143 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~--i~~g~~~~~i~CP~ 184 (561)
|+||++.+ ..+. .++|||.||..||. +... ..+.||.
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLENS---GSVKCPL 40 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHHT---SSSBTTT
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHHHhc---CCccCCc
Confidence 89999987 5565 89999999999999 4432 2678986
No 16
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.74 E-value=0.0012 Score=69.14 Aligned_cols=116 Identities=15% Similarity=0.270 Sum_probs=66.4
Q ss_pred ecHHHHHHHHHHHHHHHHHHhCCCHH--HHHHHHHHcCCChhhh--hHhh----hc--ChHHHHHHcCCC-----C-CCc
Q 008581 69 LREADIKCQQEDDITKVSTVLSISRV--DASILLRHYNWSVSKV--HDAW----FA--DEDAVRKSVGFL-----D-KPV 132 (561)
Q Consensus 69 lt~~~i~~~~~~~i~~v~~vl~i~~~--~a~~LL~~~~W~~~~l--~e~~----~~--~~~~~~~~~gl~-----~-~~~ 132 (561)
+|..|+..-+...+..|..+.-|-.+ .-..+|..|+=..+.. .+.| |. +|+ +...+-+. . .+.
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Chll~V~~ve~~~s~d~ 164 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCHLLYVDRVEVTESEDG 164 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-ceeEEEEEEEEEEecccC
Confidence 78999999998888888877666311 2234455555443321 1222 11 122 22111111 0 011
Q ss_pred ---cccCCCCccccccccccccC--CCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchh
Q 008581 133 ---VEFSNARELTCGICFDTYSC--DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 133 ---~~~~~~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
.+.......+||||++-... +-++++.|.|+|--.|+. |.+ .+||. |+....+
T Consensus 165 as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~------~scpv--cR~~q~p 223 (493)
T KOG0804|consen 165 ASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD------SSCPV--CRYCQSP 223 (493)
T ss_pred CCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc------CcChh--hhhhcCc
Confidence 11223456899999987643 334678899999999998 643 56888 8655443
No 17
>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=97.71 E-value=5.7e-06 Score=59.80 Aligned_cols=39 Identities=36% Similarity=0.820 Sum_probs=30.2
Q ss_pred cccccccccc-CCCeeeccCCCccccccce-eccCCcccccccCC
Q 008581 142 TCGICFDTYS-CDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPD 184 (561)
Q Consensus 142 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~ 184 (561)
+|+||++.+. ...++.++|||.||.+|+. |... ..+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~----~~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR----NNSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH----SSB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh----CCcCCc
Confidence 5999999985 4667789999999999999 4332 238987
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.64 E-value=1.9e-05 Score=57.11 Aligned_cols=41 Identities=37% Similarity=1.043 Sum_probs=32.9
Q ss_pred ccccccccc-cCCCeeeccCCCccccccce-eccCCcccccccCCCCCC
Q 008581 142 TCGICFDTY-SCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCC 188 (561)
Q Consensus 142 ~C~IC~e~~-~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~ 188 (561)
.|+||++.+ +...++.++|||.||..|+. +. + ..+.||. |+
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 499999998 33467789999999999999 54 2 3689998 75
No 19
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=2.1e-05 Score=80.13 Aligned_cols=44 Identities=43% Similarity=0.934 Sum_probs=36.4
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCC
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~ 189 (561)
...+.|+||++.+ ..+..++|||.||..|+. +.. ..+.||. |+.
T Consensus 11 ~~~~~C~iC~~~~--~~p~~l~C~H~~c~~C~~~~~~----~~~~Cp~--cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYF--REPVLLPCGHNFCRACLTRSWE----GPLSCPV--CRP 55 (386)
T ss_pred cccccChhhHHHh--hcCccccccchHhHHHHHHhcC----CCcCCcc--cCC
Confidence 4578999999998 566889999999999999 333 3699998 884
No 20
>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=97.55 E-value=2.3e-05 Score=58.26 Aligned_cols=45 Identities=33% Similarity=0.813 Sum_probs=35.0
Q ss_pred ccccccccccccCCCeeeccCCCc-cccccce-eccCCcccccccCCCCCCCcch
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHP-FCRACWR-VNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
...|.||++.. .+++.++|||. ||..|+. +... ..+||. |+..|.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~----~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR----KKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT----TSBBTT--TTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc----CCCCCc--CChhhc
Confidence 46799999975 67888999999 9999999 4332 578998 988764
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.44 E-value=0.00013 Score=72.00 Aligned_cols=49 Identities=22% Similarity=0.593 Sum_probs=36.0
Q ss_pred CCccccccccccccCCC------eeeccCCCccccccce-eccCCcccccccCCCCCCCcch
Q 008581 138 ARELTCGICFDTYSCDK------VVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
.....|+||++.+.... .+.++|+|.||..|+. |... ...||. |+..+.
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 34678999999764322 2456799999999999 6543 357999 988764
No 22
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.34 E-value=6.9e-05 Score=79.13 Aligned_cols=65 Identities=28% Similarity=0.568 Sum_probs=47.4
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhh-HHhhhCChHHHHHHHH
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQD-MIDMLASDEDKKKYSR 210 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~-~i~~ll~~e~~~ky~~ 210 (561)
...+.|+||++.+ ..++.++|||.||..|+. +... ...||. |+..+... +..+.+..++++.|..
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~----~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSN----QPKCPL--CRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhC----CCCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence 4468999999988 778889999999999999 3332 237998 99887543 3334445566676653
No 23
>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=97.30 E-value=7.7e-05 Score=53.16 Aligned_cols=42 Identities=33% Similarity=0.810 Sum_probs=30.5
Q ss_pred ccccccccccCCCee-eccCCCccccccce-eccCCcccccccCCCCCCCc
Q 008581 142 TCGICFDTYSCDKVV-SAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAA 190 (561)
Q Consensus 142 ~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~ 190 (561)
+|+||++.+ ..++ ..+|||.||..|+. +... ...+||. |+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCCC--CCCc
Confidence 499999987 3444 45599999999999 4332 2567987 8754
No 24
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00011 Score=70.90 Aligned_cols=55 Identities=31% Similarity=0.615 Sum_probs=42.5
Q ss_pred CCCccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhhHH
Q 008581 137 NARELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
....|.|.||+|.. .+++...|||.||-.|+- |.+-.. ..-.||. |+..|+.+.|
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~-~~~~cPV--CK~~Vs~~~v 99 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRP-NSKECPV--CKAEVSIDTV 99 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcC-CCeeCCc--cccccccceE
Confidence 46689999999976 889999999999999999 543221 2456888 8888766544
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.17 E-value=7e-05 Score=74.26 Aligned_cols=50 Identities=22% Similarity=0.622 Sum_probs=40.1
Q ss_pred CccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhhHH
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
....|.+|++.. .++..+||||.||-.|+. |-... -.||. |+..+.+..+
T Consensus 238 a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek----~eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEK----AECPL--CREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHccc----cCCCc--ccccCCCcce
Confidence 357899999975 788899999999999999 54432 23999 9998877654
No 26
>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=97.17 E-value=0.00015 Score=56.31 Aligned_cols=46 Identities=13% Similarity=0.194 Sum_probs=36.8
Q ss_pred cccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhH
Q 008581 141 LTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDM 195 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~ 195 (561)
+.|+||.+.+ .+++.++|||.||+.|+. +.. ...||. |+..++...
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~-----~~~cP~--~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS-----HGTDPV--TGQPLTHED 49 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH-----CCCCCC--CcCCCChhh
Confidence 6799999987 678999999999999999 433 247998 777775443
No 27
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.16 E-value=0.0001 Score=74.16 Aligned_cols=62 Identities=32% Similarity=0.752 Sum_probs=48.0
Q ss_pred CccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHh-hhCChHHHHHHH
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMID-MLASDEDKKKYS 209 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~-~ll~~e~~~ky~ 209 (561)
..+.|.||++.| .-++.+||+|.||.-||+ ++. ...||. |...+.+..++ +.+..++++-|.
T Consensus 22 ~lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~-----~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSY-----KPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHh--cCceeccccchHHHHHHHHHhcc-----CCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 357899999998 677788999999999999 544 356998 99998776664 455567776654
No 28
>PHA02926 zinc finger-like protein; Provisional
Probab=97.02 E-value=0.00021 Score=68.41 Aligned_cols=53 Identities=26% Similarity=0.599 Sum_probs=35.9
Q ss_pred CCccccccccccccC-----C--CeeeccCCCccccccce-eccCC-c-ccccccCCCCCCCcch
Q 008581 138 ARELTCGICFDTYSC-----D--KVVSAACGHPFCRACWR-VNDGP-G-CLMLRCPDPSCCAAVG 192 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~-----~--~~~~l~CgH~fC~~C~~-i~~g~-~-~~~i~CP~~~C~~~v~ 192 (561)
+...+|+||++..-. . -.+..+|+|.||..|++ |.... . ...-.||. |+..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI--CRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCC--Ccceee
Confidence 456889999987421 1 12345799999999999 65421 1 12457999 987653
No 29
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00013 Score=77.72 Aligned_cols=58 Identities=24% Similarity=0.469 Sum_probs=44.6
Q ss_pred ccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHhhhCC
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMIDMLAS 201 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~ 201 (561)
...||||++.. .-++.+.|||.||-.|+- |+.+.-.....||. |...|.+..+..+.-
T Consensus 186 ~~~CPICL~~~--~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPP--SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCC--CcccccccCceeeHHHHHHHHhhhcccCCccCCc--hhhhccccceeeeee
Confidence 67899999975 445556699999999999 66654345789999 999998766655443
No 30
>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=96.92 E-value=0.00023 Score=48.76 Aligned_cols=37 Identities=38% Similarity=0.850 Sum_probs=28.9
Q ss_pred cccccccccCCCeeeccCCCccccccce-eccCCcccccccCC
Q 008581 143 CGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPD 184 (561)
Q Consensus 143 C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~ 184 (561)
|+||++.. ..++.++|||.||..|+. +... ....||.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~~---~~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLKS---GNNTCPI 38 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHHh---CcCCCCC
Confidence 78999874 678889999999999999 4331 2467885
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.80 E-value=0.00055 Score=69.57 Aligned_cols=52 Identities=27% Similarity=0.712 Sum_probs=36.6
Q ss_pred cccccccccc-ccCCC---eeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHhh
Q 008581 140 ELTCGICFDT-YSCDK---VVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMIDM 198 (561)
Q Consensus 140 ~~~C~IC~e~-~~~~~---~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~~ 198 (561)
...||||... +.... ++. +|||.||.+|+. +..+ ...||. |+..+....++.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~----~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRG----SGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCC----CCCCCC--CCCccchhhccc
Confidence 3579999985 32222 233 799999999999 4443 358997 999887665543
No 32
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.39 E-value=0.0013 Score=50.68 Aligned_cols=43 Identities=37% Similarity=0.818 Sum_probs=21.3
Q ss_pred ccccccccccccCCCeee-ccCCCccccccceeccCCcccccccCCCCCCCcc
Q 008581 140 ELTCGICFDTYSCDKVVS-AACGHPFCRACWRVNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v 191 (561)
.+.|++|.+.+ ..|+. ..|.|.||..|++..- ...||. |..+.
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~-----~~~CPv--C~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCI-----GSECPV--CHTPA 50 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGT-----TTB-SS--S--B-
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhc-----CCCCCC--cCChH
Confidence 46799999987 78876 4699999999998221 234998 87664
No 33
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.29 E-value=0.00059 Score=76.13 Aligned_cols=54 Identities=30% Similarity=0.776 Sum_probs=42.9
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHhhh
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMIDML 199 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~~l 199 (561)
...++||+|.+-. .+.+...|||.||..|++ +... .-+||. |+..|.+..|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR----qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR----QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh----cCCCCC--CCCCCCccccccc
Confidence 3468999999654 788888999999999999 5432 468998 9999988777553
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=96.23 E-value=0.0017 Score=52.32 Aligned_cols=49 Identities=16% Similarity=0.131 Sum_probs=35.2
Q ss_pred CccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhh
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQD 194 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~ 194 (561)
..|.|+|+.+.. .+|+.+++||.|++.||. |... ....||. |+..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~---~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ---NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT---TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc---CCCCCCC--CCCcCCcc
Confidence 478999999987 899999999999999999 3322 1467998 77777654
No 35
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.22 E-value=0.01 Score=42.60 Aligned_cols=41 Identities=20% Similarity=0.406 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhhcChH
Q 008581 79 EDDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWFADED 119 (561)
Q Consensus 79 ~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~ 119 (561)
++.|.+.+++.++++..|..+|...+||.+..++.||.+++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 36789999999999999999999999999999999998653
No 36
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0022 Score=63.08 Aligned_cols=52 Identities=25% Similarity=0.568 Sum_probs=39.7
Q ss_pred CccccccccccccCCCeeeccCCCcccccccee-ccCCcccccccCCCCCCCcchhhHH
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWRV-NDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i-~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
..+.|.||++.. ..+..++|||.||..|+-+ .... ..-.||. |+..+.+..|
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 367899999975 7888999999999999994 2221 1345998 9988766655
No 37
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.0085 Score=62.39 Aligned_cols=42 Identities=33% Similarity=0.951 Sum_probs=37.5
Q ss_pred HhcCCCCCC--CCcceeecCCCCceEeCCCCcchhhhhhhcCccC
Q 008581 289 LANSKPCPK--CKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSD 331 (561)
Q Consensus 289 ~~ntK~CP~--C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~ 331 (561)
.++..-||+ |..|+-...|++-..|. .|.+.||.+|...|+.
T Consensus 270 msdv~yCPr~~Cq~p~~~d~~~~l~~Cs-kCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 270 MSDVVYCPRACCQLPVKQDPGRALAICS-KCNFAFCTLCKLTWHG 313 (445)
T ss_pred hcccccCChhhccCccccCchhhhhhhc-cCccHHHHHHHHhhcC
Confidence 356799998 99999668999999999 8999999999998864
No 38
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.51 E-value=0.0049 Score=61.50 Aligned_cols=51 Identities=24% Similarity=0.597 Sum_probs=40.7
Q ss_pred CCccccccccccccCC-CeeeccCCCccccccce-eccCCcccccccCCCCCCCcchh
Q 008581 138 ARELTCGICFDTYSCD-KVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~-~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
.....|.||++.+... ..+.+||.|.|...|+. |-.+ ...+||. |+..++|
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 4458899999988654 45679999999999999 5444 2678998 9998875
No 39
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.49 E-value=0.0063 Score=60.89 Aligned_cols=51 Identities=24% Similarity=0.528 Sum_probs=39.7
Q ss_pred CccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHh
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMID 197 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~ 197 (561)
....|+||+.+- .-++.++|+|.||..|++ +..+ ...||. |+..|+...+.
T Consensus 6 ~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~nd----k~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 6 KKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKND----KKTCAV--CRFPIDSTIDF 58 (324)
T ss_pred cCCcceeeeccC--CcCccccccchhhhhhhcchhhcC----CCCCce--ecCCCCcchhc
Confidence 356799999875 567899999999999999 3332 346988 99998766543
No 40
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.42 E-value=0.0076 Score=46.05 Aligned_cols=45 Identities=27% Similarity=0.609 Sum_probs=29.1
Q ss_pred CccccccccccccCCCeee-ccCCCccccccce--eccCCcccccccCCCCCC
Q 008581 139 RELTCGICFDTYSCDKVVS-AACGHPFCRACWR--VNDGPGCLMLRCPDPSCC 188 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~ 188 (561)
-.+.|||....+ .+|+. ..|||.|.++.+. +..+ ..++||..+|.
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~~~---~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQRN---GSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCTTT---S-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHHhc---CCCCCCCCCCC
Confidence 368899999877 67765 6899999999999 6333 37999999995
No 41
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.32 E-value=0.012 Score=60.97 Aligned_cols=46 Identities=26% Similarity=0.567 Sum_probs=35.4
Q ss_pred cccccccccccCCC-eeeccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 141 LTCGICFDTYSCDK-VVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 141 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
.+|.||+|+|...+ +..|||+|.|...|+. |-... .-.||. |+.-+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCCC--CCCcC
Confidence 69999999986654 5679999999999999 53321 346999 77644
No 42
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.98 E-value=0.016 Score=57.35 Aligned_cols=49 Identities=22% Similarity=0.495 Sum_probs=35.7
Q ss_pred CCCccccccccccccCCCee-eccCCCccccccce--eccCCcccccccCCCCCCCcch
Q 008581 137 NARELTCGICFDTYSCDKVV-SAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
.....+|++|-+.. +.|. ..+|||.||--|+. ..-. ..+.||. |+..+.
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 34568999998753 4454 45699999999999 2221 2689998 988765
No 43
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.023 Score=60.52 Aligned_cols=42 Identities=24% Similarity=0.743 Sum_probs=34.3
Q ss_pred CCceecCCCCCCCeeecccCCCCceeEecCCcccccccCcccCCCC
Q 008581 221 RKTKWCPAPGCEHAIDFAAGSGNFDVSCLCSYNFCWNCTEEAHRPV 266 (561)
Q Consensus 221 ~~~~~CP~~~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~ 266 (561)
...+.||. |...|... .+...++|.|++.||+.|+.+|+...
T Consensus 304 ~~wr~Cpk--C~~~ie~~--~GCnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCPK--CKFMIELS--EGCNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCcc--cceeeeec--CCcceEEeeccccchhhcCcchhhCC
Confidence 45678997 99888764 45889999999999999999886543
No 44
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.49 E-value=0.016 Score=57.52 Aligned_cols=62 Identities=26% Similarity=0.498 Sum_probs=43.0
Q ss_pred CccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHHh-hhCChHHHHHHH
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMID-MLASDEDKKKYS 209 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i~-~ll~~e~~~ky~ 209 (561)
....|-||-+-+ .-++..+|||.||.-||+ +.. ..-||. |+.......++ ..+..++.+-|.
T Consensus 24 s~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~-----qp~CP~--Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 24 SMLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGT-----QPFCPV--CREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hHHHhhhhhhee--ecceecccccchhHHHHHHHhcC-----CCCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence 356799998877 667788999999999999 544 345887 87766444332 244445555554
No 45
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.43 E-value=0.0097 Score=55.85 Aligned_cols=34 Identities=38% Similarity=0.939 Sum_probs=29.7
Q ss_pred ccccccccccccCCCeeeccCCCccccccce--eccCC
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGP 175 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~ 175 (561)
.|.|.||-.+| ..|+...|||.||..|.. ...|.
T Consensus 196 PF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y~kg~ 231 (259)
T COG5152 196 PFLCGICKKDY--ESPVVTECGHSFCSLCAIRKYQKGD 231 (259)
T ss_pred ceeehhchhhc--cchhhhhcchhHHHHHHHHHhccCC
Confidence 58999999998 788999999999999988 65554
No 46
>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=93.99 E-value=0.029 Score=45.16 Aligned_cols=43 Identities=28% Similarity=0.546 Sum_probs=28.3
Q ss_pred ccccccccccccC-----------CCeeeccCCCccccccce-eccCCcccccccCCCCCC
Q 008581 140 ELTCGICFDTYSC-----------DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCC 188 (561)
Q Consensus 140 ~~~C~IC~e~~~~-----------~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~ 188 (561)
.-.|.||++.+.. -.+...+|||.|...|+. |-... -.||. |+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~----~~CP~--CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN----NTCPL--CR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS----SB-TT--SS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC----CcCCC--CC
Confidence 3459999998721 122345799999999999 54332 28997 64
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.64 E-value=0.023 Score=41.52 Aligned_cols=43 Identities=26% Similarity=0.755 Sum_probs=20.4
Q ss_pred cccccccccCCC--eeeccCCCccccccce-eccCCcccccccCCCCCCCc
Q 008581 143 CGICFDTYSCDK--VVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAA 190 (561)
Q Consensus 143 C~IC~e~~~~~~--~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~ 190 (561)
|++|.+....++ +..-+||+.+|..||. |.... .-+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~---~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENE---GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhcc---CCCCCC--CCCC
Confidence 789998875443 3455699999999999 54421 347987 8764
No 48
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.33 E-value=0.017 Score=61.61 Aligned_cols=55 Identities=31% Similarity=0.742 Sum_probs=40.3
Q ss_pred CCCCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhh
Q 008581 136 SNARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQD 194 (561)
Q Consensus 136 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~ 194 (561)
.+.+...|++|-+.- .+++-..|.|.||+-|++ +..-.....+.||. |-..++.+
T Consensus 532 enk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPV--CHIGLSID 588 (791)
T ss_pred cccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcc--cccccccc
Confidence 356678999999854 778888999999999998 32211113589998 87766544
No 49
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.13 E-value=0.052 Score=57.69 Aligned_cols=47 Identities=28% Similarity=0.723 Sum_probs=37.8
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchh
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
.+.|.|.||+..+ -.+++++|||.||..|+. .+. ...||. |+..+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r~ld~-----~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDRSLDQ-----ETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHHHhcc-----CCCCcc--ccccccc
Confidence 5689999999887 678888999999999977 332 456887 9887753
No 50
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=92.97 E-value=0.097 Score=52.73 Aligned_cols=93 Identities=25% Similarity=0.676 Sum_probs=55.0
Q ss_pred cCCCccccccce-eccCCccccc-ccCCCCCCCcchhhHHhhhCChHHHHHHHHHHHHHHHhcCCCceecCCCCCCCeee
Q 008581 159 ACGHPFCRACWR-VNDGPGCLML-RCPDPSCCAAVGQDMIDMLASDEDKKKYSRYLLRSYVEDNRKTKWCPAPGCEHAID 236 (561)
Q Consensus 159 ~CgH~fC~~C~~-i~~g~~~~~i-~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~ 236 (561)
.||-.||+.|.. ...|.-...+ .=-...|...+++... ...+|...... .| ....+.||. |..+.+
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a-------~~arwd~as~~-TI--k~tTkpCPk--ChvptE 408 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAA-------EQARWDAASKE-TI--KKTTKPCPK--CHVPTE 408 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccccceeeecChhhh-------hhhhhhhhhhh-hh--hhccCCCCC--ccCccc
Confidence 499999999999 3333200000 0011235555554332 23445443222 12 234567886 988877
Q ss_pred cccCCCCceeEe-c--CCcccccccCcccCCC
Q 008581 237 FAAGSGNFDVSC-L--CSYNFCWNCTEEAHRP 265 (561)
Q Consensus 237 ~~~~~~~~~v~C-~--C~~~fC~~C~~~~H~p 265 (561)
.. .+...+.| . ||..+||.|+-+|.+.
T Consensus 409 rn--GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 409 RN--GGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred cC--CceEEeecCCCCCCceeEeccCChhhhh
Confidence 64 56788999 4 9999999999998653
No 51
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.85 E-value=0.05 Score=56.64 Aligned_cols=54 Identities=28% Similarity=0.616 Sum_probs=36.9
Q ss_pred CCCCccccccccccccCCC-----eee-ccCCCccccccce-eccCC---cccccccCCCCCCCcc
Q 008581 136 SNARELTCGICFDTYSCDK-----VVS-AACGHPFCRACWR-VNDGP---GCLMLRCPDPSCCAAV 191 (561)
Q Consensus 136 ~~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~-i~~g~---~~~~i~CP~~~C~~~v 191 (561)
+.....+|+||++...... .-. .+|.|.||..|++ |.... ....-.||. |+...
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~s 220 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVPS 220 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCcc
Confidence 3466889999999864332 112 4599999999999 65321 123578998 88753
No 52
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.68 E-value=0.0084 Score=61.28 Aligned_cols=47 Identities=26% Similarity=0.704 Sum_probs=33.8
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
...+.|+||++.+. .-+....|.|.||.+||- ...+ .-.||. |+..+
T Consensus 41 ~~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~g----n~ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRSG----NNECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHhc----CCCCch--HHhhc
Confidence 34789999999873 223445699999999998 4333 346887 87654
No 53
>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=91.92 E-value=0.074 Score=33.78 Aligned_cols=24 Identities=29% Similarity=0.928 Sum_probs=16.7
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
|.||.|+..|-. +-+.|. .|||.|
T Consensus 1 K~CP~C~~~V~~----~~~~Cp-~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE----SAKFCP-HCGYDF 24 (26)
T ss_pred CcCCCCcCCchh----hcCcCC-CCCCCC
Confidence 679999988862 225565 677776
No 54
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.49 E-value=0.092 Score=54.14 Aligned_cols=65 Identities=20% Similarity=0.490 Sum_probs=44.7
Q ss_pred HHHHcCCCCCCccccC---CCCccccccccccccCCCeeeccCCCc-cccccce-eccCCcccccccCCCCCCCcchh
Q 008581 121 VRKSVGFLDKPVVEFS---NARELTCGICFDTYSCDKVVSAACGHP-FCRACWR-VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 121 ~~~~~gl~~~~~~~~~---~~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
+++..||..+...... +.....|-||+.+. .+++.|||.|. .|.+|-+ +. ...=.||. |++.|..
T Consensus 268 LqEiyGien~~v~~~~~~~~~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr----~q~n~CPI--CRqpi~~ 337 (349)
T KOG4265|consen 268 LQEIYGIENSTVEGTDADESESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR----YQTNNCPI--CRQPIEE 337 (349)
T ss_pred eehhhccccCCCCCCccccccCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH----HhhcCCCc--cccchHh
Confidence 4456677544322222 24467899999876 78899999996 8999998 32 11335998 9988754
No 55
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.71 E-value=0.14 Score=50.09 Aligned_cols=54 Identities=26% Similarity=0.581 Sum_probs=38.6
Q ss_pred cccccccccccCCCeeeccCCCccccccceeccCCcccccccCCCCCCCcchhhHHhhhCC
Q 008581 141 LTCGICFDTYSCDKVVSAACGHPFCRACWRVNDGPGCLMLRCPDPSCCAAVGQDMIDMLAS 201 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~ 201 (561)
+.|..|+--.+...++.+.|+|.||..|.+...+. .||. |+..+....+..-++
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~-----~C~l--Ckk~ir~i~l~~slp 57 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPD-----VCPL--CKKSIRIIQLNRSLP 57 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCcc-----cccc--ccceeeeeecccccc
Confidence 56898987766566677899999999999944332 7988 998765444433343
No 56
>PRK00420 hypothetical protein; Validated
Probab=90.04 E-value=3.6 Score=35.92 Aligned_cols=19 Identities=16% Similarity=0.170 Sum_probs=13.9
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 008581 413 QLKFIIDAWLQIVECRRVL 431 (561)
Q Consensus 413 ~~~fl~~a~~~l~~~r~~L 431 (561)
.++.|..++..|.+.++.+
T Consensus 93 ri~Ei~~~l~~l~ki~~~~ 111 (112)
T PRK00420 93 RITEIIRYLEVLERIRKIK 111 (112)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 4567778888888877754
No 57
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=89.71 E-value=0.093 Score=52.55 Aligned_cols=37 Identities=24% Similarity=0.828 Sum_probs=28.7
Q ss_pred hcCCCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCC
Q 008581 290 ANSKPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 290 ~ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
.++.+|-=|-...+ |-+|. +|||-|||-|...|-.-.
T Consensus 237 ~a~~kC~LCLe~~~------~pSaT-pCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 237 EATRKCSLCLENRS------NPSAT-PCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCCCceEEEecCCC------CCCcC-cCcchHHHHHHHHHHccc
Confidence 45667777766665 47898 799999999999996544
No 58
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=89.63 E-value=0.11 Score=53.38 Aligned_cols=48 Identities=27% Similarity=0.574 Sum_probs=36.0
Q ss_pred CCcccccccccc-ccC----------CCeeeccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 138 ARELTCGICFDT-YSC----------DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 138 ~~~~~C~IC~e~-~~~----------~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
.+..+|.||+|+ +.. ..|..+||||.+-..|++ |-+. .-.||. |+.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER----qQTCPI--Cr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER----QQTCPI--CRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh----ccCCCc--ccCcc
Confidence 346789999998 221 124578999999999999 7664 347998 98875
No 59
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.27 E-value=0.34 Score=52.92 Aligned_cols=35 Identities=23% Similarity=0.639 Sum_probs=30.1
Q ss_pred CCCCcceee-cCCCCceEeCCCCcchhhhhhhcCccCC
Q 008581 296 PKCKRPIEK-NQGCMHMTCSPPCKFEFCWLCLGAWSDH 332 (561)
Q Consensus 296 P~C~~~IEK-~~GCnhm~C~~~C~~~FCw~C~~~w~~h 332 (561)
|.|+..+.- .+.+.-+.|. |++.|||.|+.+|+.-
T Consensus 164 ~~C~~av~~~~~~~~~v~C~--~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 164 PGCGLAVKFGSLESVEVDCG--CGHEFCFACGEESHSP 199 (444)
T ss_pred CCCCceeeccCCCccceeCC--CCchhHhhccccccCC
Confidence 579999987 7889999997 9999999999888543
No 60
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=88.58 E-value=0.24 Score=37.24 Aligned_cols=46 Identities=28% Similarity=0.513 Sum_probs=31.6
Q ss_pred ccccccccccccCCCeeeccCCCccccccceeccCCcccccccCCCCCCCcchhh
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWRVNDGPGCLMLRCPDPSCCAAVGQD 194 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v~~~ 194 (561)
...|-.|...- ...+.++|||..|..||-..+- -.||. |...+...
T Consensus 7 ~~~~~~~~~~~--~~~~~~pCgH~I~~~~f~~~rY-----ngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVG--TKGTVLPCGHLICDNCFPGERY-----NGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEccccc--cccccccccceeeccccChhhc-----cCCCC--CCCcccCC
Confidence 34566665443 5567789999999999984332 24888 88877543
No 61
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.47 E-value=0.26 Score=49.48 Aligned_cols=43 Identities=30% Similarity=0.743 Sum_probs=33.6
Q ss_pred ccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
.|-|.||-..+ ..+|...|+|+||..|.. ...+. +|+. |...+
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk~~-----~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQKGE-----KCYV--CSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhccccccCC-----ccee--ccccc
Confidence 46799999988 788999999999999988 55443 4655 66543
No 62
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=87.02 E-value=0.37 Score=51.61 Aligned_cols=47 Identities=30% Similarity=0.747 Sum_probs=34.5
Q ss_pred CCCccccccccccccCCCeee-ccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 137 NARELTCGICFDTYSCDKVVS-AACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
......|++|.... .+++. ..|||.||..|+. +... ...||. |...+
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~----~~~cp~--~~~~~ 66 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN----HQKCPV--CRQEL 66 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc----CcCCcc--ccccc
Confidence 45578999999877 56666 5999999999999 3222 456876 65544
No 63
>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=86.97 E-value=18 Score=37.25 Aligned_cols=34 Identities=26% Similarity=0.650 Sum_probs=21.4
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~ 328 (561)
..||.|+...-.|..=.-|. . .|||.||-.|+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i-~-~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMV-N-VCGHTLCESCVDL 37 (309)
T ss_pred CCCCcCCCCCccCccccccc-C-CCCCcccHHHHHH
Confidence 57999998544332211122 1 3888899899876
No 64
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.10 E-value=0.4 Score=29.51 Aligned_cols=10 Identities=50% Similarity=1.122 Sum_probs=8.4
Q ss_pred CCCCCCccee
Q 008581 294 PCPKCKRPIE 303 (561)
Q Consensus 294 ~CP~C~~~IE 303 (561)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 4899998887
No 65
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.91 E-value=0.98 Score=47.39 Aligned_cols=56 Identities=14% Similarity=0.306 Sum_probs=39.3
Q ss_pred CccccccccccccC-CCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhhHHh
Q 008581 139 RELTCGICFDTYSC-DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMID 197 (561)
Q Consensus 139 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i~ 197 (561)
+.|.|||=-+.-.. +.|..+.|||..|++-+. +..+. ...++||- |.........+
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng-~~sfKCPY--CP~e~~~~~~k 390 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNG-SQSFKCPY--CPVEQLASDTK 390 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCC-CeeeeCCC--CCcccCHHhcc
Confidence 46899995544332 556789999999999999 43332 24799998 98766554443
No 66
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=85.60 E-value=0.24 Score=51.53 Aligned_cols=44 Identities=30% Similarity=0.634 Sum_probs=33.1
Q ss_pred cccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCC
Q 008581 141 LTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCC 188 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~ 188 (561)
..|-||-+.- .++..-||||..|..|+. |.+..+ .-.||.+.|.
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~sd~--gq~CPFCRcE 414 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDSDE--GQTCPFCRCE 414 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhcccCC--CCCCCceeeE
Confidence 4599999854 677778999999999999 765432 3579984443
No 67
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.45 E-value=0.47 Score=30.06 Aligned_cols=11 Identities=36% Similarity=0.930 Sum_probs=9.1
Q ss_pred CCCCCCCccee
Q 008581 293 KPCPKCKRPIE 303 (561)
Q Consensus 293 K~CP~C~~~IE 303 (561)
+.||+|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 68999998776
No 68
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.09 E-value=0.58 Score=46.40 Aligned_cols=70 Identities=21% Similarity=0.458 Sum_probs=46.5
Q ss_pred HHHHHHcCCCCCCccccCCCCccccccccccccCC--------CeeeccCCCccccccce-e-ccCCcccccccCCCCCC
Q 008581 119 DAVRKSVGFLDKPVVEFSNARELTCGICFDTYSCD--------KVVSAACGHPFCRACWR-V-NDGPGCLMLRCPDPSCC 188 (561)
Q Consensus 119 ~~~~~~~gl~~~~~~~~~~~~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~-i-~~g~~~~~i~CP~~~C~ 188 (561)
+.+...+|...+...+....+...|.||-..+..+ ++..++|+|.|-..|++ | --|+ .-.||- |+
T Consensus 203 d~mAs~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGK---kqtCPY--CK 277 (328)
T KOG1734|consen 203 DYMASTIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGK---KQTCPY--CK 277 (328)
T ss_pred HHHHHHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecC---CCCCch--HH
Confidence 44555666655444444444567899998765432 46789999999999999 2 1232 457998 98
Q ss_pred Ccchh
Q 008581 189 AAVGQ 193 (561)
Q Consensus 189 ~~v~~ 193 (561)
..++.
T Consensus 278 ekVdl 282 (328)
T KOG1734|consen 278 EKVDL 282 (328)
T ss_pred HHhhH
Confidence 87753
No 69
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.96 E-value=0.34 Score=50.75 Aligned_cols=48 Identities=35% Similarity=0.800 Sum_probs=36.8
Q ss_pred ccccccccccccC---CCeeeccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 140 ELTCGICFDTYSC---DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 140 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
..+||||++.+.. ..++++.|||-|=.+|++ |- + ......||. |...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl-~-k~~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWL-G-KKTKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHH-h-hhhhhhCcc--cCChh
Confidence 4689999998632 456789999999999999 44 3 245789999 87643
No 70
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=84.70 E-value=0.64 Score=34.38 Aligned_cols=27 Identities=30% Similarity=0.725 Sum_probs=20.3
Q ss_pred CCCCCCCcceeecC--CCCceEeCCCCcch
Q 008581 293 KPCPKCKRPIEKNQ--GCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~IEK~~--GCnhm~C~~~C~~~ 320 (561)
+-||.|+.++.... +-++..|+ .|++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~-~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCR-KCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECC-cCCCe
Confidence 46999998887653 35688998 78864
No 71
>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=84.66 E-value=0.3 Score=47.49 Aligned_cols=48 Identities=23% Similarity=0.638 Sum_probs=34.5
Q ss_pred ccccccccc-ccCCCeee--cc-CCCccccccce-e-ccCCcccccccCCCCCCCcch
Q 008581 141 LTCGICFDT-YSCDKVVS--AA-CGHPFCRACWR-V-NDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 141 ~~C~IC~e~-~~~~~~~~--l~-CgH~fC~~C~~-i-~~g~~~~~i~CP~~~C~~~v~ 192 (561)
-.||||-.+ |-.-++.. -| |-|..|.+|+- | ..| +-.||-++|+.++.
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~G----pAqCP~~gC~kILR 64 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRG----PAQCPYKGCGKILR 64 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCC----CCCCCCccHHHHHH
Confidence 469999865 32223322 23 99999999999 4 444 57899999998764
No 72
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=83.95 E-value=0.47 Score=33.78 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=21.3
Q ss_pred CCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCC
Q 008581 295 CPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 295 CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
||-|...+. +.++=. |||.||..|+..|....
T Consensus 1 CpiC~~~~~-----~Pv~l~--CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLP--CGHSFCRSCLERLWKEP 32 (42)
T ss_dssp ETTTTSB-S-----SEEE-S--SSSEEEHHHHHHHHCCS
T ss_pred CCccchhhC-----CccccC--CcCHHHHHHHHHHHHcc
Confidence 566666655 235554 99999999998765544
No 73
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=83.86 E-value=0.89 Score=54.31 Aligned_cols=68 Identities=28% Similarity=0.533 Sum_probs=47.9
Q ss_pred cccccccccc-ccCCCeeeccCCCccccccce-e----ccCCcc--cccccCCCCCCCcchhhHHhhhCChHHHHHHHH
Q 008581 140 ELTCGICFDT-YSCDKVVSAACGHPFCRACWR-V----NDGPGC--LMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSR 210 (561)
Q Consensus 140 ~~~C~IC~e~-~~~~~~~~l~CgH~fC~~C~~-i----~~g~~~--~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~ 210 (561)
.-.|.|||.+ +.....+.|.|+|.|-..|.+ + ..|+.+ ..+.||. |...|..-.++.++.+ +.+.|+.
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP-iKel~ed 3561 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP-IKELYED 3561 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH-HHHHHHH
Confidence 4579999966 333445679999999999998 2 124433 3689999 9999988877777753 3444443
No 74
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.85 E-value=0.23 Score=55.68 Aligned_cols=44 Identities=27% Similarity=0.659 Sum_probs=33.6
Q ss_pred ccccccccccccCC---CeeeccCCCccccccce-eccCCcccccccCCCCCCC
Q 008581 140 ELTCGICFDTYSCD---KVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 140 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~ 189 (561)
...|.||.+..... .+..++|+|.||..|++ |-+. .-.||. |+.
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er----~qtCP~--CR~ 338 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER----QQTCPT--CRT 338 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH----hCcCCc--chh
Confidence 57899999986321 15678999999999999 6543 457988 766
No 75
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.73 E-value=1 Score=46.33 Aligned_cols=54 Identities=24% Similarity=0.567 Sum_probs=37.6
Q ss_pred ccccccccccccCC----CeeeccCCCccccccce-eccCCcccccccCCCCCCCc--chhhHHhh
Q 008581 140 ELTCGICFDTYSCD----KVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAA--VGQDMIDM 198 (561)
Q Consensus 140 ~~~C~IC~e~~~~~----~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~--v~~~~i~~ 198 (561)
.+.|.||-++|... -|..+.|||.+|..|+. +-.. ..+.||. |+.. ++...++.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~---~~i~cpf--cR~~~~~~~~~~~~ 63 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN---SRILCPF--CRETTEIPDGDVKS 63 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC---ceeeccC--CCCcccCCchhHhh
Confidence 46799999998654 24457799999999999 3222 2577876 9887 44444433
No 76
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.69 E-value=0.25 Score=49.42 Aligned_cols=39 Identities=36% Similarity=0.824 Sum_probs=29.7
Q ss_pred ccccccccccccCCCeeeccCCCc-cccccce-eccCCcccccccCCCCCCCc
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHP-FCRACWR-VNDGPGCLMLRCPDPSCCAA 190 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~-i~~g~~~~~i~CP~~~C~~~ 190 (561)
...|.||++.. .+.+.|+|||. .|..|-+ ++ .||. |++.
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGkrm~--------eCPI--CRqy 340 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGKRMN--------ECPI--CRQY 340 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhccccc--------cCch--HHHH
Confidence 67899999975 78899999994 5776655 43 6887 8654
No 77
>PHA00626 hypothetical protein
Probab=83.37 E-value=0.83 Score=34.30 Aligned_cols=30 Identities=27% Similarity=0.575 Sum_probs=22.0
Q ss_pred CCCCCCc-ceeecCCCCc----eEeCCCCcchhhhh
Q 008581 294 PCPKCKR-PIEKNQGCMH----MTCSPPCKFEFCWL 324 (561)
Q Consensus 294 ~CP~C~~-~IEK~~GCnh----m~C~~~C~~~FCw~ 324 (561)
.||+|+. -|-|++-|+. -.|. .||+.|=-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCk-dCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCC-DCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcC-CCCCeechh
Confidence 5999998 4878777665 6777 788777433
No 78
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=82.62 E-value=0.31 Score=49.67 Aligned_cols=53 Identities=21% Similarity=0.640 Sum_probs=39.6
Q ss_pred ccccccccccccC--CCeeeccCCCccccccce-eccCCcccccccCCCCCCCcchhhHHh
Q 008581 140 ELTCGICFDTYSC--DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMID 197 (561)
Q Consensus 140 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i~ 197 (561)
.-.||+|.+.... ..++..+||-..|.-||. |.+.. .=+||. |+.....+-|+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~l---ngrcpa--crr~y~denv~ 69 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNL---NGRCPA--CRRKYDDENVR 69 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhc---cCCChH--hhhhcccccee
Confidence 4459999997543 456678899999999999 76653 568999 98876555443
No 79
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=82.23 E-value=0.66 Score=36.08 Aligned_cols=25 Identities=32% Similarity=0.817 Sum_probs=11.0
Q ss_pred CCCCCCCcceeec---CCCCceEeCCCCc
Q 008581 293 KPCPKCKRPIEKN---QGCMHMTCSPPCK 318 (561)
Q Consensus 293 K~CP~C~~~IEK~---~GCnhm~C~~~C~ 318 (561)
-+|++|...+... +||-|++|+ .|-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs-~Ci 35 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCS-SCI 35 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-T-TTG
T ss_pred cCCcHHHHHhcCCceeccCccHHHH-HHh
Confidence 6899998876642 666666666 454
No 80
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=81.33 E-value=1.7 Score=28.83 Aligned_cols=29 Identities=28% Similarity=0.680 Sum_probs=18.7
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
+.+-||+|+.+.....+=--|.|. .|++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~-~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCP-SCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEES-SSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECC-CCcCE
Confidence 458899999999988886778897 78864
No 81
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=81.00 E-value=0.33 Score=49.57 Aligned_cols=46 Identities=26% Similarity=0.701 Sum_probs=33.3
Q ss_pred CCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
....+|.+|-..+. +.+....|-|.||++||- +.. ...||. |...|
T Consensus 13 n~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~-----~~~CP~--C~i~i 60 (331)
T KOG2660|consen 13 NPHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEE-----SKYCPT--CDIVI 60 (331)
T ss_pred ccceehhhccceee-cchhHHHHHHHHHHHHHHHHHHH-----hccCCc--cceec
Confidence 34789999987652 333445699999999998 543 357998 77765
No 82
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=80.92 E-value=1.3 Score=31.50 Aligned_cols=32 Identities=28% Similarity=0.601 Sum_probs=23.5
Q ss_pred HHHHhcCCCCCCCCcceeecCCCCceEeCC-CCcchh
Q 008581 286 NWILANSKPCPKCKRPIEKNQGCMHMTCSP-PCKFEF 321 (561)
Q Consensus 286 ~wi~~ntK~CP~C~~~IEK~~GCnhm~C~~-~C~~~F 321 (561)
.|.+...+.||+|+..- |+--+.|++ .|.+.|
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 46666779999999865 777788873 566554
No 83
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=80.86 E-value=0.53 Score=53.74 Aligned_cols=45 Identities=31% Similarity=0.786 Sum_probs=34.7
Q ss_pred cccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchh
Q 008581 141 LTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
+.|+||.+ .+.++..+|+|.||.+||. |.... ...||. |+..+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~---~~~~~~--cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE---NAPCPL--CRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc---CCCCcH--HHHHHHH
Confidence 89999999 3788889999999999999 54432 227777 8765543
No 84
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.64 E-value=0.64 Score=47.71 Aligned_cols=50 Identities=26% Similarity=0.535 Sum_probs=34.8
Q ss_pred cCCCCccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchh
Q 008581 135 FSNARELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 135 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
.|..+.-.|+||+-.. -..+..||+|.-|.+|+. +... ..|-. |+.++..
T Consensus 417 lp~sEd~lCpICyA~p--i~Avf~PC~H~SC~~CI~qHlmN~-----k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAGP--INAVFAPCSHRSCYGCITQHLMNC-----KRCFF--CKTTVID 468 (489)
T ss_pred CCCcccccCcceeccc--chhhccCCCCchHHHHHHHHHhcC-----CeeeE--ecceeee
Confidence 3556678899999753 344567999999999999 3222 34644 8776644
No 85
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.45 E-value=0.66 Score=45.23 Aligned_cols=20 Identities=40% Similarity=1.057 Sum_probs=15.9
Q ss_pred eEeCCCCcchhhhhhhcCccCCC
Q 008581 311 MTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 311 m~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
+|| |||-|||-|+-.|-.+.
T Consensus 62 vTl---CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL---CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee---cccceehHHHHHHHhhc
Confidence 555 99999999998887655
No 86
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=80.19 E-value=0.85 Score=37.64 Aligned_cols=33 Identities=24% Similarity=0.389 Sum_probs=23.0
Q ss_pred eeccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 156 VSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 156 ~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
+.-.|+|.|...||. |-+... ..-.||. |++.+
T Consensus 48 v~g~C~H~FH~hCI~kWl~~~~-~~~~CPm--CR~~w 81 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILKWLSTQS-SKGQCPM--CRQPW 81 (85)
T ss_pred eeccCccHHHHHHHHHHHcccc-CCCCCCC--cCCee
Confidence 334699999999999 433221 2458998 98765
No 87
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=79.70 E-value=0.9 Score=36.18 Aligned_cols=51 Identities=25% Similarity=0.669 Sum_probs=20.1
Q ss_pred cccccccccccc-CCCe-e----eccCCCccccccce-e----ccCCccc---ccccCCCCCCCcch
Q 008581 140 ELTCGICFDTYS-CDKV-V----SAACGHPFCRACWR-V----NDGPGCL---MLRCPDPSCCAAVG 192 (561)
Q Consensus 140 ~~~C~IC~e~~~-~~~~-~----~l~CgH~fC~~C~~-i----~~g~~~~---~i~CP~~~C~~~v~ 192 (561)
...|+||+.... .... . ...|++.|-..|+. | ..+...+ .=.||. |+..|.
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 467999998753 2222 1 12588999999999 2 2221111 236998 988774
No 88
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.58 E-value=1.1 Score=51.00 Aligned_cols=23 Identities=30% Similarity=0.743 Sum_probs=14.5
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~ 328 (561)
+.||+|+..+. =+..||-.||..
T Consensus 28 ~~Cp~CG~~~~-------------~~~~fC~~CG~~ 50 (645)
T PRK14559 28 KPCPQCGTEVP-------------VDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCCCC-------------cccccccccCCc
Confidence 46777777655 244477777754
No 89
>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=79.18 E-value=0.44 Score=42.66 Aligned_cols=32 Identities=38% Similarity=0.749 Sum_probs=26.8
Q ss_pred ccccccccccccC-CCeeeccCC------Cccccccce-e
Q 008581 140 ELTCGICFDTYSC-DKVVSAACG------HPFCRACWR-V 171 (561)
Q Consensus 140 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~-i 171 (561)
..+|.||++.... .-++.++|| |.||.+|++ |
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 6889999998866 456778887 789999999 6
No 90
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=78.16 E-value=0.43 Score=53.64 Aligned_cols=46 Identities=20% Similarity=0.385 Sum_probs=23.5
Q ss_pred cccccccccccCCCe-eeccCCCccccccce-eccCCcccccccCCCCCCCcch
Q 008581 141 LTCGICFDTYSCDKV-VSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~-~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
-.|++|+..+..... ....|+|+||..|+. |... .-.||. |+..|.
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~----aqTCPi--DR~EF~ 171 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC----AQTCPV--DRGEFG 171 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh----cccCch--hhhhhh
Confidence 346666554422111 124577777777776 5432 234665 665543
No 91
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=78.14 E-value=0.97 Score=43.19 Aligned_cols=31 Identities=26% Similarity=0.863 Sum_probs=23.8
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCcc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWS 330 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~ 330 (561)
-.||-|...+.. -.-. .|||.|||.|+..|.
T Consensus 19 ~~CpICld~~~d------PVvT-~CGH~FC~~CI~~wl 49 (193)
T PLN03208 19 FDCNICLDQVRD------PVVT-LCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCccCCCcCCC------cEEc-CCCchhHHHHHHHHH
Confidence 579999887642 2334 599999999999884
No 92
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.55 E-value=0.94 Score=45.46 Aligned_cols=41 Identities=32% Similarity=0.928 Sum_probs=31.0
Q ss_pred cccccccccccCCCeeec-cCCCccccccce--eccCCcccccccCCCCCCC
Q 008581 141 LTCGICFDTYSCDKVVSA-ACGHPFCRACWR--VNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~ 189 (561)
+.|+.|-... .+++.. .|+|.||..|+. +-+. .+.||. |..
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds----Df~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS----DFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc----cccCCC--ccc
Confidence 7899998776 445444 599999999999 4332 578998 754
No 93
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=77.30 E-value=2.2 Score=29.45 Aligned_cols=29 Identities=28% Similarity=0.677 Sum_probs=21.6
Q ss_pred eecCCCCCCCeeecccC---CCCceeEe-cCCccc
Q 008581 224 KWCPAPGCEHAIDFAAG---SGNFDVSC-LCSYNF 254 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~---~~~~~v~C-~C~~~f 254 (561)
..||+ |+........ .+...|.| .|++.|
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57987 9988876543 34568899 899876
No 94
>PLN03086 PRLI-interacting factor K; Provisional
Probab=76.46 E-value=3.6 Score=45.91 Aligned_cols=57 Identities=21% Similarity=0.473 Sum_probs=34.3
Q ss_pred cccccCCCCCCCcchhhHHhhhCChHHHHHHHHHHHHHHHhcCCCceecCCCCCCCeeecccCCCCceeEe-cCCccc
Q 008581 178 LMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSRYLLRSYVEDNRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNF 254 (561)
Q Consensus 178 ~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~f 254 (561)
..+.||. |...++...+.... ..-..+.+.||..+|+..+..... ...+.| .|+..|
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe----------------~~C~r~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHE----------------AYCSRHNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF 463 (567)
T ss_pred CeEECCC--CCCccchhHHHHHH----------------hhCCCcceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence 3578998 98887665442110 011234578998789988865422 234567 776655
No 95
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.29 E-value=0.76 Score=49.24 Aligned_cols=51 Identities=27% Similarity=0.494 Sum_probs=36.0
Q ss_pred CCccccccccccccCC-----C----------eeeccCCCccccccce-eccCCcccccccCCCCCCCcchh
Q 008581 138 ARELTCGICFDTYSCD-----K----------VVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~-----~----------~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
.....|.||+...+.. . ....||.|.|-..|+. |.++- .+.||. |+.++++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y---kl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY---KLICPV--CRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh---cccCCc--cCCCCCC
Confidence 3456799999875421 1 1124899999999999 76653 578998 7776653
No 96
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=74.03 E-value=7.2 Score=40.05 Aligned_cols=98 Identities=18% Similarity=0.319 Sum_probs=52.6
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhhcChHHHHHHcCCCCCCcc-c---------cCCCCcccccccccc
Q 008581 80 DDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWFADEDAVRKSVGFLDKPVV-E---------FSNARELTCGICFDT 149 (561)
Q Consensus 80 ~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~-~---------~~~~~~~~C~IC~e~ 149 (561)
..+..|..+++---..+...|+ .++=|+........+-++.++++. + ......-.|+||+..
T Consensus 238 ~~~~~v~~~~stgl~~~vFflq--------fldWWyssd~~~~~k~~l~~p~PpPPh~~~~se~e~l~~~~~~CpvClk~ 309 (357)
T KOG0826|consen 238 KAVRGVAFSLSTGLSVGVFFLQ--------FLDWWYSSDNQRKIKSTLDPPIPPPPHKQYNSESELLPPDREVCPVCLKK 309 (357)
T ss_pred HHHhhHHHHHHhhHHHHHHHHH--------HHHHHhcchHHHhhccCCCCCCCcCChhhcccccccCCCccccChhHHhc
Confidence 3334444444444455566666 555576544433333344222111 1 012235679999976
Q ss_pred ccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 150 YSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 150 ~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
.. ++.+..--|-.||-.|+- +.. .-.||..+|...+
T Consensus 310 r~-Nptvl~vSGyVfCY~Ci~~Yv~~-----~~~CPVT~~p~~v 347 (357)
T KOG0826|consen 310 RQ-NPTVLEVSGYVFCYPCIFSYVVN-----YGHCPVTGYPASV 347 (357)
T ss_pred cC-CCceEEecceEEeHHHHHHHHHh-----cCCCCccCCcchH
Confidence 52 333333358899999998 442 2358887776543
No 97
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=73.77 E-value=2.5 Score=42.19 Aligned_cols=10 Identities=30% Similarity=0.541 Sum_probs=6.9
Q ss_pred ccccCCCCCC
Q 008581 5 EDDFYSGEAM 14 (561)
Q Consensus 5 ~~~~~~~~~~ 14 (561)
+|+||.++..
T Consensus 24 ~de~~~~~~~ 33 (240)
T PF05764_consen 24 EDEFFWNQYG 33 (240)
T ss_pred hhhhhhhhcc
Confidence 4788877554
No 98
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.19 E-value=1.3 Score=44.14 Aligned_cols=34 Identities=32% Similarity=0.788 Sum_probs=28.1
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcC-ccCCC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGA-WSDHG 333 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~-w~~h~ 333 (561)
.+|+-|-..++. -.|+ .|||-|||.|+-- |..-.
T Consensus 216 ~kC~lC~e~~~~------ps~t-~CgHlFC~~Cl~~~~t~~k 250 (271)
T COG5574 216 YKCFLCLEEPEV------PSCT-PCGHLFCLSCLLISWTKKK 250 (271)
T ss_pred cceeeeecccCC------cccc-cccchhhHHHHHHHHHhhc
Confidence 679999988885 6788 7999999999976 76443
No 99
>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=73.18 E-value=2.5 Score=27.84 Aligned_cols=27 Identities=26% Similarity=0.771 Sum_probs=13.9
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
-+||+|+....-.+|.+ |.|. .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp-~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCP-ECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEET-TTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCC-cccccC
Confidence 47999998877766665 6887 898875
No 100
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=73.08 E-value=3 Score=42.61 Aligned_cols=22 Identities=27% Similarity=0.649 Sum_probs=18.2
Q ss_pred CCceeEe-cCCcccccccCcccC
Q 008581 242 GNFDVSC-LCSYNFCWNCTEEAH 263 (561)
Q Consensus 242 ~~~~v~C-~C~~~fC~~C~~~~H 263 (561)
....++| .|+..||..|..-.|
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred CCCcEEchhccceeeccchHHHH
Confidence 3456789 999999999987666
No 101
>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=73.08 E-value=1.3 Score=30.75 Aligned_cols=32 Identities=25% Similarity=0.833 Sum_probs=21.6
Q ss_pred CCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCC
Q 008581 295 CPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDH 332 (561)
Q Consensus 295 CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h 332 (561)
||-|...+.. .+.-. .|||.||+.|...|...
T Consensus 1 C~iC~~~~~~-----~~~~~-~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD-----PVVVT-PCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS-----EEEEC-TTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC-----cCEEC-CCCCchhHHHHHHHHHC
Confidence 5666555442 34566 69999999999887544
No 102
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.39 E-value=0.83 Score=47.60 Aligned_cols=54 Identities=26% Similarity=0.554 Sum_probs=36.6
Q ss_pred ccccccccccccCC-Ceeecc-CCCccccccce-eccCCcccccccCCCCCCCcchhhHH
Q 008581 140 ELTCGICFDTYSCD-KVVSAA-CGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 140 ~~~C~IC~e~~~~~-~~~~l~-CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
.-.|.||-+.+|.. ++.++. |||.|-..|+. |.++... .-.||. |+..++...+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps-~R~cpi--c~ik~~~r~~ 60 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS-NRGCPI--CQIKLQERHV 60 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCc-cCCCCc--eeecccceee
Confidence 35799997776653 444565 99999999999 7666421 247988 7754444333
No 103
>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=72.36 E-value=3.5 Score=28.88 Aligned_cols=30 Identities=20% Similarity=0.569 Sum_probs=25.2
Q ss_pred CCCCCCCCcc-eeecCCCCceEeCCCCcchhhhhhhcCc
Q 008581 292 SKPCPKCKRP-IEKNQGCMHMTCSPPCKFEFCWLCLGAW 329 (561)
Q Consensus 292 tK~CP~C~~~-IEK~~GCnhm~C~~~C~~~FCw~C~~~w 329 (561)
...|+.|... +. ++|. .|+..+|..|...-
T Consensus 3 ~~~C~~H~~~~~~-------~~C~-~C~~~~C~~C~~~~ 33 (42)
T PF00643_consen 3 EPKCPEHPEEPLS-------LFCE-DCNEPLCSECTVSG 33 (42)
T ss_dssp SSB-SSTTTSBEE-------EEET-TTTEEEEHHHHHTS
T ss_pred CccCccCCccceE-------EEec-CCCCccCccCCCCC
Confidence 3689999988 77 9999 89999999998753
No 104
>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=71.86 E-value=11 Score=25.81 Aligned_cols=33 Identities=27% Similarity=0.366 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhH
Q 008581 79 EDDITKVSTVLSISRVDASILLRHYNWSVSKVHD 112 (561)
Q Consensus 79 ~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e 112 (561)
.+.|.++.+. |.++..|+..|+..+||++..++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 4568888888 99999999999999999987664
No 105
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=71.75 E-value=2.8 Score=47.80 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=9.3
Q ss_pred CCCCCCCcceee
Q 008581 293 KPCPKCKRPIEK 304 (561)
Q Consensus 293 K~CP~C~~~IEK 304 (561)
+.||+|+..+-+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 889998887653
No 106
>PHA02926 zinc finger-like protein; Provisional
Probab=70.85 E-value=2.9 Score=40.65 Aligned_cols=53 Identities=23% Similarity=0.487 Sum_probs=33.4
Q ss_pred CCCCCCCCcce-eec-CCCCc-eEeCCCCcchhhhhhhcCccCCCCCCCCcccCCcc
Q 008581 292 SKPCPKCKRPI-EKN-QGCMH-MTCSPPCKFEFCWLCLGAWSDHGERTGGFYACNRY 345 (561)
Q Consensus 292 tK~CP~C~~~I-EK~-~GCnh-m~C~~~C~~~FCw~C~~~w~~h~~~~g~~y~C~~~ 345 (561)
-+.|+-|-..+ +|. .++.. -.= +.|+|-||+.|...|......+|.-..|+-=
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL-~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiC 225 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLL-DSCNHIFCITCINIWHRTRRETGASDNCPIC 225 (242)
T ss_pred CCCCccCcccccccccccccccccc-CCCCchHHHHHHHHHHHhccccCcCCcCCCC
Confidence 38899998665 331 11210 011 2699999999999998754344555667743
No 107
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=70.74 E-value=7 Score=38.84 Aligned_cols=73 Identities=25% Similarity=0.624 Sum_probs=42.1
Q ss_pred CCccccccccccccCCCeeeccCCCc-cccccce---eccC-CcccccccCCCCCCCcchhhHHhhhCChHHHHHHHHHH
Q 008581 138 ARELTCGICFDTYSCDKVVSAACGHP-FCRACWR---VNDG-PGCLMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSRYL 212 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~---i~~g-~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l 212 (561)
....+|-+|......+.- .=.|. -|..|-+ |... ++..-++|| |+..+ -
T Consensus 63 ~p~v~CrVCq~~I~i~gk---~~QhVVkC~~CnEATPIr~aPpGKKYVRCP---CNCLL---------I----------- 116 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGK---MHQHVVKCSVCNEATPIRNAPPGKKYVRCP---CNCLL---------I----------- 116 (256)
T ss_pred CceEEeecCCceecccCc---cceeeEECCCCCccccccCCCCCCeeEecC---CceEE---------E-----------
Confidence 346889999866432111 01221 3566666 6543 345578999 43322 0
Q ss_pred HHHHHhcCCCceecCCCCCCCeeecccC
Q 008581 213 LRSYVEDNRKTKWCPAPGCEHAIDFAAG 240 (561)
Q Consensus 213 ~~~~v~~~~~~~~CP~~~C~~~i~~~~~ 240 (561)
- .......-||.|+|.++|...+.
T Consensus 117 C----k~sS~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 117 C----KSSSQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred e----ecccccccCCCCCCcceEEeCCc
Confidence 0 11234568999999999987543
No 108
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=70.59 E-value=1.6 Score=32.36 Aligned_cols=28 Identities=21% Similarity=0.616 Sum_probs=20.2
Q ss_pred cCCCCCCCCc-ceeecCCCCceEeCCCCcchh
Q 008581 291 NSKPCPKCKR-PIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 291 ntK~CP~C~~-~IEK~~GCnhm~C~~~C~~~F 321 (561)
+-+.||+|+. .+.... +.++|. .|++.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~-~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCG-KCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECC-CcCCEE
Confidence 3479999988 444333 689998 898764
No 109
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.99 E-value=1.3 Score=41.45 Aligned_cols=30 Identities=37% Similarity=0.960 Sum_probs=21.8
Q ss_pred ecCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCCCccee
Q 008581 248 CLCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKCKRPIE 303 (561)
Q Consensus 248 C~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C~~~IE 303 (561)
=+|||.||..|.+.+ ..++.+||-|++-|-
T Consensus 149 TkCGHvFC~~Cik~a--------------------------lk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKDA--------------------------LKNTNKCPTCRKKIT 178 (187)
T ss_pred cccchhHHHHHHHHH--------------------------HHhCCCCCCcccccc
Confidence 389999999996431 123489999997654
No 110
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=69.98 E-value=4.1 Score=43.47 Aligned_cols=11 Identities=18% Similarity=0.839 Sum_probs=6.8
Q ss_pred cCCCCcccccc
Q 008581 135 FSNARELTCGI 145 (561)
Q Consensus 135 ~~~~~~~~C~I 145 (561)
.|.+..|.|+-
T Consensus 189 LPDSTDFVCGT 199 (458)
T PF10446_consen 189 LPDSTDFVCGT 199 (458)
T ss_pred CCCcccccCCC
Confidence 45566677764
No 111
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=69.69 E-value=2.6 Score=37.19 Aligned_cols=58 Identities=17% Similarity=0.249 Sum_probs=33.0
Q ss_pred eeEecCCcccccccCcccC--CCCCchh-HHHHHHHh-HhhhHhHHHHHhcCCCCCCCCccee
Q 008581 245 DVSCLCSYNFCWNCTEEAH--RPVDCGT-VAKWILKN-CAESENMNWILANSKPCPKCKRPIE 303 (561)
Q Consensus 245 ~v~C~C~~~fC~~C~~~~H--~p~~C~~-~~~~~~k~-~~~~~~~~wi~~ntK~CP~C~~~IE 303 (561)
.+.|.||++||-. .+.|. ....-.. ..+..+-. ..+....+|+...--.||.|+.+.+
T Consensus 70 v~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 70 VIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred EEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 4579999999976 44553 2221111 11111111 1223345787776679999999887
No 112
>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=69.37 E-value=4.4 Score=27.64 Aligned_cols=26 Identities=19% Similarity=0.451 Sum_probs=23.2
Q ss_pred CCCCCCc-ceeecCCCCceEeCCCCcchhhhhhhc
Q 008581 294 PCPKCKR-PIEKNQGCMHMTCSPPCKFEFCWLCLG 327 (561)
Q Consensus 294 ~CP~C~~-~IEK~~GCnhm~C~~~C~~~FCw~C~~ 327 (561)
.||.|+. ++. ++|. .|+...|..|..
T Consensus 2 ~C~~H~~~~~~-------~fC~-~~~~~iC~~C~~ 28 (39)
T cd00021 2 LCDEHGEEPLS-------LFCE-TDRALLCVDCDL 28 (39)
T ss_pred CCCccCCcceE-------EEeC-ccChhhhhhcCh
Confidence 5899987 888 9999 899999999964
No 113
>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=69.24 E-value=3.1 Score=35.42 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=26.0
Q ss_pred ccccccccccccCCCeeeccCCCccccccce
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR 170 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 170 (561)
.-.|++|...+....++..||||.|...|.+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4569999998877777788999999999974
No 114
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=69.08 E-value=3.8 Score=29.58 Aligned_cols=28 Identities=21% Similarity=0.643 Sum_probs=19.7
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
-.||+|+..++-..+=..++|. .||..+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp-~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCP-YCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECC-CCCCeE
Confidence 4799999888765443367887 777654
No 115
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.57 E-value=0.55 Score=35.06 Aligned_cols=43 Identities=33% Similarity=0.621 Sum_probs=30.4
Q ss_pred cccccccccccCCCeeeccCCCc-cccccce--eccCCcccccccCCCCCCCcc
Q 008581 141 LTCGICFDTYSCDKVVSAACGHP-FCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
-+|.||++.. -+.+.-.|||. .|-+|-. +..+ .-.||. |+.+|
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~~----~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKAL----HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHcc----CCcCcc--hhhHH
Confidence 5799999864 45555679996 7888876 3322 346888 87765
No 116
>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=67.14 E-value=3.9 Score=41.24 Aligned_cols=49 Identities=22% Similarity=0.604 Sum_probs=31.7
Q ss_pred cccccccc-ccCCCee--eccCCCccccccce-eccCCcccccccCCCCCCCcchhhH
Q 008581 142 TCGICFDT-YSCDKVV--SAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDM 195 (561)
Q Consensus 142 ~C~IC~e~-~~~~~~~--~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~ 195 (561)
.||+|-.. |-.-+++ .-+|+|..|.+|+- |..- .+..||. |..++...-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~---g~~~Cpe--C~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL---GPAQCPE--CMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc---CCCCCCc--ccchhhhcc
Confidence 48888754 3222222 22799999999999 4332 1567995 988775443
No 117
>PF04641 Rtf2: Rtf2 RING-finger
Probab=67.05 E-value=3.7 Score=41.44 Aligned_cols=67 Identities=19% Similarity=0.417 Sum_probs=44.3
Q ss_pred CCCccccccccccccC-CCeee-ccCCCccccccce-eccCCcccccccCCCCCCCcchhhHHhhhCC-hHHHHHHHH
Q 008581 137 NARELTCGICFDTYSC-DKVVS-AACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMIDMLAS-DEDKKKYSR 210 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~-~~~~~-l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~-~e~~~ky~~ 210 (561)
....+.|||....+.. ..++. .+|||.|+..+++ +. . .-.||. |...+....|-.|-+ .+.++....
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~---~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~~ 180 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--K---SKKCPV--CGKPFTEEDIIPLNPPEEELEKLRE 180 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--c---cccccc--cCCccccCCEEEecCCccHHHHHHH
Confidence 3567999999988743 23444 4899999999999 64 1 235998 999987655443333 234444433
No 118
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.83 E-value=6.1 Score=27.08 Aligned_cols=29 Identities=24% Similarity=0.586 Sum_probs=20.6
Q ss_pred eecCCCCCCCeeecccC---CCCceeEe-cCCccc
Q 008581 224 KWCPAPGCEHAIDFAAG---SGNFDVSC-LCSYNF 254 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~---~~~~~v~C-~C~~~f 254 (561)
..||+ |.....+... .....|.| .|++.|
T Consensus 3 i~Cp~--C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN--CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC--CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 56887 9887776532 34467899 899876
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=65.60 E-value=6 Score=34.50 Aligned_cols=39 Identities=21% Similarity=0.608 Sum_probs=25.2
Q ss_pred eecCCCCCCCeeecccC------CCCceeEe-cCCcccccccCcccCC
Q 008581 224 KWCPAPGCEHAIDFAAG------SGNFDVSC-LCSYNFCWNCTEEAHR 264 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~ 264 (561)
..|-+ |...+...+. .......| .|+..||..|..-+|.
T Consensus 56 ~~C~~--C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCFG--CQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred CcccC--cCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 45765 7765542211 11234579 9999999999887774
No 120
>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=65.07 E-value=3.7 Score=28.24 Aligned_cols=26 Identities=27% Similarity=0.784 Sum_probs=15.5
Q ss_pred CCCCCCcceeec------CCCCceEeCCCCcchh
Q 008581 294 PCPKCKRPIEKN------QGCMHMTCSPPCKFEF 321 (561)
Q Consensus 294 ~CP~C~~~IEK~------~GCnhm~C~~~C~~~F 321 (561)
.||+|+..+.-. .| ..+.|. .|++.|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~-~~v~C~-~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANG-GKVRCG-KCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCC-CEEECC-CCCCEE
Confidence 578887755422 12 267777 677654
No 121
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=64.53 E-value=12 Score=44.36 Aligned_cols=19 Identities=5% Similarity=0.156 Sum_probs=10.7
Q ss_pred ccccceEE---ecHHHHHHHHH
Q 008581 61 RQQHSYTV---LREADIKCQQE 79 (561)
Q Consensus 61 ~~~~~y~v---lt~~~i~~~~~ 79 (561)
..+.+|++ -|.+++...+.
T Consensus 415 ~~elPftf~~P~s~eel~~lL~ 436 (840)
T PF04147_consen 415 KSELPFTFPCPSSHEELLELLD 436 (840)
T ss_pred ccCCCceecCCCCHHHHHHHHh
Confidence 44667776 45555554443
No 122
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=63.27 E-value=9.7 Score=27.02 Aligned_cols=30 Identities=27% Similarity=0.984 Sum_probs=20.3
Q ss_pred HHHHHhcCCCCCCCCcceee-cCCCCceEeCCCCc
Q 008581 285 MNWILANSKPCPKCKRPIEK-NQGCMHMTCSPPCK 318 (561)
Q Consensus 285 ~~wi~~ntK~CP~C~~~IEK-~~GCnhm~C~~~C~ 318 (561)
.+|...+ ..||.|+.|+-+ ..| .++|. .|+
T Consensus 11 ~G~~ML~-~~Cp~C~~PL~~~k~g--~~~Cv-~C~ 41 (41)
T PF06677_consen 11 QGWTMLD-EHCPDCGTPLMRDKDG--KIYCV-SCG 41 (41)
T ss_pred HhHhHhc-CccCCCCCeeEEecCC--CEECC-CCC
Confidence 3453333 689999999988 444 57776 563
No 123
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=62.94 E-value=5.4 Score=31.69 Aligned_cols=50 Identities=28% Similarity=0.571 Sum_probs=29.6
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcch-----hhhhhhcCccCCCCCCCCcccCCcch
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKFE-----FCWLCLGAWSDHGERTGGFYACNRYE 346 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~~-----FCw~C~~~w~~h~~~~g~~y~C~~~~ 346 (561)
.||.|+.+++..+ .+.+|. .|+.. +|--|+.+......-..--|.|+.-.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~-~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE-ACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET-TT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT
T ss_pred cCCCCCCccEEeC--CEEECc-cccccceecccCCCcccHHHHHHHhcccceeeccCC
Confidence 6999999999988 788998 89854 69999887654432111357777543
No 124
>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=62.59 E-value=3.2 Score=30.59 Aligned_cols=40 Identities=20% Similarity=0.412 Sum_probs=27.6
Q ss_pred ccccccccccCCCeeeccCC-----Cccccccce-e-ccCCcccccccCC
Q 008581 142 TCGICFDTYSCDKVVSAACG-----HPFCRACWR-V-NDGPGCLMLRCPD 184 (561)
Q Consensus 142 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~-i-~~g~~~~~i~CP~ 184 (561)
.|-||++.....++...||. |.+-..|+. | .... ..+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~---~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG---NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC---CCcCCC
Confidence 48899984444666777885 778889998 3 3332 357887
No 125
>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=62.24 E-value=5.6 Score=29.70 Aligned_cols=28 Identities=32% Similarity=0.552 Sum_probs=17.1
Q ss_pred CCCCCCCccee------ecCCCCceE-eCCCCcchh
Q 008581 293 KPCPKCKRPIE------KNQGCMHMT-CSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IE------K~~GCnhm~-C~~~C~~~F 321 (561)
|+||.|+-.-+ .+.+..++. |. .|++..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~-~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS-TCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC-CCCCCc
Confidence 89999986554 233455554 65 565543
No 126
>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=61.78 E-value=11 Score=44.16 Aligned_cols=13 Identities=15% Similarity=0.161 Sum_probs=4.8
Q ss_pred HHHHcCCChhhhh
Q 008581 99 LLRHYNWSVSKVH 111 (561)
Q Consensus 99 LL~~~~W~~~~l~ 111 (561)
.+.+|+-.+-.|+
T Consensus 768 ~~~~Fk~RvlDLl 780 (784)
T PF04931_consen 768 NVIHFKNRVLDLL 780 (784)
T ss_pred HHHHHHHHHHHHH
Confidence 3333433333333
No 127
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=60.74 E-value=1.4 Score=49.88 Aligned_cols=52 Identities=19% Similarity=0.158 Sum_probs=32.4
Q ss_pred ccccccccccccC--CCeeecc---CCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 140 ELTCGICFDTYSC--DKVVSAA---CGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 140 ~~~C~IC~e~~~~--~~~~~l~---CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
..+|.||.-.+.. +-.-.++ |+|.+|..||. +.++.....+.|-.+.|...|
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 4556666655432 1122344 99999999999 666543345666666677655
No 128
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.64 E-value=5.4 Score=38.63 Aligned_cols=48 Identities=23% Similarity=0.602 Sum_probs=39.0
Q ss_pred ccccccccccccCCCeeeccCCCccccccce-------eccCCcccccccCCCCCCCcc
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR-------VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-------i~~g~~~~~i~CP~~~C~~~v 191 (561)
...|.+|-..+...+.+.|-|-|.|--.|+. -+..+ ..++||. |...|
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAP--aGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAP--AGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCC--CcccCCC--CCCcc
Confidence 4569999998888899999999999999999 23333 3689998 98866
No 129
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=59.95 E-value=5.7 Score=31.15 Aligned_cols=28 Identities=32% Similarity=0.795 Sum_probs=20.0
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
.++.||.|+....+...=..++|. .||+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~-~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCP-NCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcC-CCCC
Confidence 458999999999874444456776 5654
No 130
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=58.65 E-value=6.4 Score=33.18 Aligned_cols=28 Identities=29% Similarity=0.905 Sum_probs=20.6
Q ss_pred CCCCCCCcce--eecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPI--EKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~I--EK~~GCnhm~C~~~C~~~F 321 (561)
--||.|+..+ ++.+-||...|+ .|.+.|
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~-tCpY~~ 31 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCR-TCPYVF 31 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcC-CCCcee
Confidence 3699998654 444559999999 887654
No 131
>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=58.54 E-value=28 Score=23.56 Aligned_cols=35 Identities=20% Similarity=0.285 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhh
Q 008581 80 DDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWF 115 (561)
Q Consensus 80 ~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~ 115 (561)
+.|.++.+ +|.+...+...|...+||+++..+-.+
T Consensus 3 ~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 34555555 589999999999999999998876543
No 132
>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=58.28 E-value=5.7 Score=34.52 Aligned_cols=27 Identities=26% Similarity=0.680 Sum_probs=18.8
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
+.||+|++..---.- +.++|. .||..|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP-~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCP-KCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCC-CCCCcc
Confidence 689999876653222 778887 676654
No 133
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=58.12 E-value=3.5 Score=41.78 Aligned_cols=88 Identities=27% Similarity=0.576 Sum_probs=46.1
Q ss_pred CCccccccce-eccCCcccccccCCCCCCCcchhhHHhhhCChHHHHHHHHHH-HHHHHhc----CCCceecCCCCCCCe
Q 008581 161 GHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSRYL-LRSYVED----NRKTKWCPAPGCEHA 234 (561)
Q Consensus 161 gH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l-~~~~v~~----~~~~~~CP~~~C~~~ 234 (561)
|-++|..|-. +- .+++.||. |...+ +++.-+..-|..+. ++.|++. ++....|-. |...
T Consensus 307 gGy~CP~CktkVC----sLPi~CP~--Csl~L-------ilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~--CQ~~ 371 (421)
T COG5151 307 GGYECPVCKTKVC----SLPISCPI--CSLQL-------ILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFV--CQGP 371 (421)
T ss_pred CceeCCcccceee----cCCccCcc--hhHHH-------HHHHHHHHHHHhhccCcccccccCCCCCCCcccee--ccCC
Confidence 3456666655 21 14677776 64432 22222333344322 3445543 234445654 6554
Q ss_pred eecccC------CCCceeEe-cCCcccccccCcccC
Q 008581 235 IDFAAG------SGNFDVSC-LCSYNFCWNCTEEAH 263 (561)
Q Consensus 235 i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H 263 (561)
+...+. .......| .|...||..|..-.|
T Consensus 372 fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 372 FPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred CCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 433221 12345689 999999999986666
No 134
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=56.93 E-value=4.9 Score=40.94 Aligned_cols=49 Identities=20% Similarity=0.499 Sum_probs=34.0
Q ss_pred Cccccccccccc-cCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCc
Q 008581 139 RELTCGICFDTY-SCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAA 190 (561)
Q Consensus 139 ~~~~C~IC~e~~-~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~ 190 (561)
+.|+||+=-+.- ..+.|+++.|||..=+.-+. +..+ |...++||- |...
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~n-G~~~FKCPY--CP~~ 385 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQN-GVLSFKCPY--CPEM 385 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhc-CcEEeeCCC--CCcc
Confidence 358899854432 22567899999998777777 4333 346899998 8654
No 135
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=56.81 E-value=6.2 Score=45.98 Aligned_cols=27 Identities=33% Similarity=1.134 Sum_probs=23.5
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFC 322 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FC 322 (561)
..||.|+..+...+||. +|. .||+-=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~-~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH-SCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC-CCCCCCC
Confidence 36999999999999997 899 8988655
No 136
>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=56.14 E-value=2.8e+02 Score=32.36 Aligned_cols=45 Identities=13% Similarity=0.071 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcccceecccCccchhhhhHHHHHHHHHHHhHHHHHHHHHH
Q 008581 414 LKFIIDAWLQIVECRRVLKWTYAYGYYLPEHEHAKRQFFEYLQGEAESGLERLHQCAEK 472 (561)
Q Consensus 414 ~~fl~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~~e~~~e~L~~~le~ 472 (561)
++-+++-.+.|.+....| ..+.+-....|+.++.+++.|...+..
T Consensus 581 L~~l~e~~~~l~~~ae~L--------------aeR~e~a~d~Qe~L~~R~~~vl~~l~~ 625 (717)
T PF10168_consen 581 LQELQEERKSLRESAEKL--------------AERYEEAKDKQEKLMKRVDRVLQLLNS 625 (717)
T ss_pred HHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 444555555565555666 135667778899999999988876643
No 137
>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=55.97 E-value=9 Score=26.11 Aligned_cols=27 Identities=22% Similarity=0.715 Sum_probs=17.2
Q ss_pred eecCCCCCCCeeecccCCCCceeEe-cCCcc
Q 008581 224 KWCPAPGCEHAIDFAAGSGNFDVSC-LCSYN 253 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~ 253 (561)
++||. |+..+....+..... .| .|++.
T Consensus 2 ~FCp~--C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCPE--CGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BETT--TTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCCC--CCccceEcCCCccCc-CCCCCCCc
Confidence 57987 999887764443333 78 78765
No 138
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=54.08 E-value=11 Score=45.49 Aligned_cols=29 Identities=28% Similarity=0.777 Sum_probs=16.9
Q ss_pred ceecCCCCCCCeeecccCCCCceeEe-cCCccc-----ccccCcc
Q 008581 223 TKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNF-----CWNCTEE 261 (561)
Q Consensus 223 ~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~f-----C~~C~~~ 261 (561)
...||. |+..+. ...| .||... |..|+..
T Consensus 667 ~rkCPk--CG~~t~--------~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCPS--CGTETY--------ENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEECCC--CCCccc--------cccCcccCCcCCCceeCccCCCc
Confidence 367886 875431 1267 677553 6666654
No 139
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.74 E-value=9.7 Score=31.50 Aligned_cols=28 Identities=29% Similarity=0.587 Sum_probs=23.0
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
-.||.|++..-|..+=---.|+ .|++.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~-kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCR-KCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcC-CCCCee
Confidence 5899999999888887778888 677655
No 140
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.64 E-value=4.2 Score=42.26 Aligned_cols=44 Identities=27% Similarity=0.692 Sum_probs=31.2
Q ss_pred CccccccccccccCCCeeeccCCCccccccceeccCCcccccccCCCCCCCcch
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWRVNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
....|.||.+.. .+.+-+||||.-| |...... ...||- |+..|.
T Consensus 304 ~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs~~----l~~CPv--CR~rI~ 347 (355)
T KOG1571|consen 304 QPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCSKH----LPQCPV--CRQRIR 347 (355)
T ss_pred CCCceEEecCCc--cceeeecCCcEEE--chHHHhh----CCCCch--hHHHHH
Confidence 356799999976 6688899999866 6653222 345998 876553
No 141
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=53.26 E-value=7.9 Score=39.87 Aligned_cols=47 Identities=28% Similarity=0.738 Sum_probs=33.3
Q ss_pred CCCccccccccccccCCCeeeccCCCccccccceeccCCcccccccCCCCCCCcch
Q 008581 137 NARELTCGICFDTYSCDKVVSAACGHPFCRACWRVNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
....+.||||++.+. ..++...=||..|..|-.. ..-+||. |+..++
T Consensus 45 ~~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~~------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRTK------VSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCc-ccceecCCCcEehhhhhhh------hcccCCc--cccccc
Confidence 345789999999762 1222334489999999851 2567998 998887
No 142
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=52.63 E-value=7 Score=33.15 Aligned_cols=32 Identities=34% Similarity=0.779 Sum_probs=25.5
Q ss_pred CCCccccccccccccCCCeeeccCCCcccccc
Q 008581 137 NARELTCGICFDTYSCDKVVSAACGHPFCRAC 168 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 168 (561)
-..+|+|.-||=....+.+..-.=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45689999999877666666555689999999
No 143
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=52.10 E-value=37 Score=22.80 Aligned_cols=32 Identities=25% Similarity=0.270 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHh
Q 008581 81 DITKVSTVLSISRVDASILLRHYNWSVSKVHDA 113 (561)
Q Consensus 81 ~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~ 113 (561)
.|.++.+. |.++..|...|...+||+++..+-
T Consensus 4 ~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 4 KIDQLLEM-GFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHH
Confidence 44555443 899999999999999998887653
No 144
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=51.91 E-value=12 Score=27.38 Aligned_cols=27 Identities=26% Similarity=0.748 Sum_probs=16.7
Q ss_pred ecCCCCCCCeeecccCCCCceeEe-cCCcc
Q 008581 225 WCPAPGCEHAIDFAAGSGNFDVSC-LCSYN 253 (561)
Q Consensus 225 ~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~ 253 (561)
+||. |+..+............| .|++.
T Consensus 2 FCp~--Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPK--CGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCC--CCCccccccCCCCCEEECCcCCCe
Confidence 6886 988776553333335667 67754
No 145
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.75 E-value=6.1 Score=38.90 Aligned_cols=51 Identities=18% Similarity=0.277 Sum_probs=35.0
Q ss_pred CccccccccccccCCCe--eeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHH
Q 008581 139 RELTCGICFDTYSCDKV--VSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
..+.||||-+.+...-+ +.-+|||.||..|.. |.. ...||. |...+....|
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 46889999998854433 234799999999999 432 345776 6666654433
No 146
>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=51.53 E-value=9.2 Score=32.70 Aligned_cols=25 Identities=32% Similarity=0.781 Sum_probs=19.1
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
+.||+|+.++...+ +.+.|+ .|++.
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~-~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCP-SCGYE 25 (104)
T ss_pred CCCcccCcccccCC--CeEECc-CCCCc
Confidence 36999999887654 478898 78765
No 147
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=50.02 E-value=13 Score=28.98 Aligned_cols=28 Identities=36% Similarity=0.781 Sum_probs=17.0
Q ss_pred cCCCCCCCCcceee---cCCCCceEeCCCCcc
Q 008581 291 NSKPCPKCKRPIEK---NQGCMHMTCSPPCKF 319 (561)
Q Consensus 291 ntK~CP~C~~~IEK---~~GCnhm~C~~~C~~ 319 (561)
+.|+||.|+..+.. .+|=-...|. +|+.
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~-~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCN-GCES 35 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcC-CCCc
Confidence 45999999977664 2332234555 4544
No 148
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=49.59 E-value=3.7 Score=42.13 Aligned_cols=28 Identities=18% Similarity=0.571 Sum_probs=21.6
Q ss_pred CCCCCCCcceee-cCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEK-NQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK-~~GCnhm~C~~~C~~~F 321 (561)
.+||+|+..|-+ .-.=|.+.|. .|+++|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCP-KCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCC-CCCCCe
Confidence 889999988764 3445668897 899887
No 149
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=49.45 E-value=5.3 Score=45.24 Aligned_cols=52 Identities=19% Similarity=0.478 Sum_probs=37.7
Q ss_pred CccccccccccccCCCeeeccCCCccccccce--eccCCcccccccCCCCCCCcchhhHH
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAVGQDMI 196 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v~~~~i 196 (561)
...+|+||+..+ ..++.+.|.|.||..||. ..... ....||. |+..++...+
T Consensus 20 k~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~--~~~~~~l--c~~~~eK~s~ 73 (684)
T KOG4362|consen 20 KILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKK--GPKQCAL--CKSDIEKRSL 73 (684)
T ss_pred hhccCCceeEEe--eccchhhhhHHHHhhhhhceeeccC--ccccchh--hhhhhhhhhc
Confidence 367899999987 667889999999999999 21111 1677887 8766544333
No 150
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.15 E-value=13 Score=25.16 Aligned_cols=28 Identities=25% Similarity=0.771 Sum_probs=14.1
Q ss_pred eecCCCCCCCeeeccc--CCCCceeEe-cCCcc
Q 008581 224 KWCPAPGCEHAIDFAA--GSGNFDVSC-LCSYN 253 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~--~~~~~~v~C-~C~~~ 253 (561)
++||. |+..+.... +.......| .|++.
T Consensus 1 kfC~~--CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQ--CGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TT--T--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Ccccc--ccChhhhhcCCCCCccceECCCCCCE
Confidence 47887 888876643 355667788 88764
No 151
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=48.76 E-value=13 Score=39.77 Aligned_cols=7 Identities=43% Similarity=0.938 Sum_probs=3.2
Q ss_pred CcCCCCC
Q 008581 43 GFIEEDP 49 (561)
Q Consensus 43 ~f~e~~~ 49 (561)
+|.+.|+
T Consensus 108 GFAdSDD 114 (458)
T PF10446_consen 108 GFADSDD 114 (458)
T ss_pred ccccccc
Confidence 5544433
No 152
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=48.38 E-value=7.2 Score=39.28 Aligned_cols=30 Identities=30% Similarity=0.826 Sum_probs=24.1
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAW 329 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w 329 (561)
-+|--|.-.|- +-|-..|||.||++|-..+
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~h 55 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRH 55 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHH
Confidence 57888888877 7776579999999998654
No 153
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=47.73 E-value=14 Score=37.54 Aligned_cols=26 Identities=38% Similarity=0.933 Sum_probs=22.1
Q ss_pred CCCCCCCCcceeec--CCCCceEeCCCCc
Q 008581 292 SKPCPKCKRPIEKN--QGCMHMTCSPPCK 318 (561)
Q Consensus 292 tK~CP~C~~~IEK~--~GCnhm~C~~~C~ 318 (561)
-++|+.|+.+|+|. +|=+--+|. .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP-~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCP-VCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCC-CCC
Confidence 37999999999984 888888887 786
No 154
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.71 E-value=14 Score=43.67 Aligned_cols=33 Identities=27% Similarity=0.671 Sum_probs=21.4
Q ss_pred CCCceecCCCCCCCeeecccCCCCceeEe-cCCc-----ccccccCccc
Q 008581 220 NRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSY-----NFCWNCTEEA 262 (561)
Q Consensus 220 ~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~-----~fC~~C~~~~ 262 (561)
....+.||. |+... ....| .||. .||..|+...
T Consensus 623 EVg~RfCps--CG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 623 EIGRRKCPS--CGKET--------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred cccCccCCC--CCCcC--------CcccCCCCCCCCCcceeCccccCcC
Confidence 345678997 87542 33578 7884 4788886543
No 155
>PHA02929 N1R/p28-like protein; Provisional
Probab=47.45 E-value=10 Score=37.77 Aligned_cols=40 Identities=20% Similarity=0.565 Sum_probs=27.8
Q ss_pred CCCCCCCCcceeecCCCCc---eEeCCCCcchhhhhhhcCccCCC
Q 008581 292 SKPCPKCKRPIEKNQGCMH---MTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnh---m~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
...||-|...+.....-+. +.- .|+|.||..|...|....
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~~~ 216 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKKEK 216 (238)
T ss_pred CCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHhcC
Confidence 4689999988764332221 222 499999999999997644
No 156
>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=46.80 E-value=15 Score=31.60 Aligned_cols=26 Identities=35% Similarity=0.996 Sum_probs=16.7
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
-+||+|+...-=..|=+ +.|. .|+|+
T Consensus 3 p~CP~C~seytY~dg~~-~iCp-eC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP-SCLYE 28 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc-ccccc
Confidence 58999987665444443 5665 56554
No 157
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=46.79 E-value=13 Score=44.30 Aligned_cols=16 Identities=25% Similarity=0.447 Sum_probs=8.5
Q ss_pred HHHHHHHHHHhHHHHH
Q 008581 452 FEYLQGEAESGLERLH 467 (561)
Q Consensus 452 fe~~Q~~~e~~~e~L~ 467 (561)
||-.|....+..|+|.
T Consensus 2419 FEtKer~Fnka~EK~R 2434 (3015)
T KOG0943|consen 2419 FETKERKFNKAMEKLR 2434 (3015)
T ss_pred cchHHHHHHHHHHHHH
Confidence 5555555555555554
No 158
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=46.75 E-value=12 Score=33.52 Aligned_cols=23 Identities=39% Similarity=0.804 Sum_probs=19.0
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhh
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCL 326 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~ 326 (561)
+-||.|+.|+.+ .-|.-||.+|+
T Consensus 29 ~hCp~Cg~PLF~-----------KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR-----------KDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCccee-----------eCCeEECCCCC
Confidence 789999999985 47777777886
No 159
>PHA03096 p28-like protein; Provisional
Probab=46.71 E-value=4.6 Score=41.26 Aligned_cols=30 Identities=27% Similarity=0.564 Sum_probs=22.1
Q ss_pred cccccccccccCC----Cee-ec-cCCCccccccce
Q 008581 141 LTCGICFDTYSCD----KVV-SA-ACGHPFCRACWR 170 (561)
Q Consensus 141 ~~C~IC~e~~~~~----~~~-~l-~CgH~fC~~C~~ 170 (561)
..|+||++..-.. ..+ .| .|.|.||..|++
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~ 214 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIK 214 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHH
Confidence 6799999875322 122 23 499999999999
No 160
>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=46.55 E-value=15 Score=23.85 Aligned_cols=25 Identities=32% Similarity=0.784 Sum_probs=14.2
Q ss_pred CCCCCCCcceeec--CCCCceEeCCCCc
Q 008581 293 KPCPKCKRPIEKN--QGCMHMTCSPPCK 318 (561)
Q Consensus 293 K~CP~C~~~IEK~--~GCnhm~C~~~C~ 318 (561)
++||.|+.+|++. +|=+...|. .|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~-rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP-RCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T-TTC
T ss_pred CcCccCCCcceEeEecCCCCeECc-CCc
Confidence 6899999999763 455556665 564
No 161
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.19 E-value=7.8 Score=38.85 Aligned_cols=25 Identities=24% Similarity=0.543 Sum_probs=20.1
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcchhhhhhh
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCL 326 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~ 326 (561)
.|+.+... .+++|. .|....|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~-~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCE-EDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEec-ccccccCCCCC
Confidence 56666655 459999 89999999997
No 162
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=45.71 E-value=9.3 Score=39.40 Aligned_cols=49 Identities=24% Similarity=0.619 Sum_probs=33.2
Q ss_pred CCCccccccccccccCCCeeeccCCCccccccce-eccCCcccccccCCCCCCCcc
Q 008581 137 NARELTCGICFDTYSCDKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
+.....|.||.... +-...+||+|..|..|-- ...- .....||. |+...
T Consensus 58 DEen~~C~ICA~~~--TYs~~~PC~H~~CH~Ca~RlRAL--Y~~K~C~~--CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGST--TYSARYPCGHQICHACAVRLRAL--YMQKGCPL--CRTET 107 (493)
T ss_pred ccccceeEEecCCc--eEEEeccCCchHHHHHHHHHHHH--HhccCCCc--ccccc
Confidence 44578899999865 444568999999999976 1100 11346887 87643
No 163
>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=45.42 E-value=4.7 Score=41.24 Aligned_cols=28 Identities=21% Similarity=0.565 Sum_probs=20.5
Q ss_pred CCCCCCCcceeec-CCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKN-QGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~-~GCnhm~C~~~C~~~F 321 (561)
.+||+|+..|-+. -.=|.+.|. .|+|+|
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCP-KCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCC-CCCCcC
Confidence 7899998887753 334567887 788875
No 164
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.09 E-value=13 Score=37.33 Aligned_cols=49 Identities=24% Similarity=0.655 Sum_probs=34.5
Q ss_pred CccccccccccccCCCeeeccC----CCccccccce--eccCCcccccccCC-CCCCC
Q 008581 139 RELTCGICFDTYSCDKVVSAAC----GHPFCRACWR--VNDGPGCLMLRCPD-PSCCA 189 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~C----gH~fC~~C~~--i~~g~~~~~i~CP~-~~C~~ 189 (561)
..+.|.+|-+.+ +++..+.| .|.||.-|-+ |........+.||. .+|..
T Consensus 267 apLcCTLC~ERL--EDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPL 322 (352)
T KOG3579|consen 267 APLCCTLCHERL--EDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPL 322 (352)
T ss_pred Cceeehhhhhhh--ccCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcc
Confidence 358899999988 44444445 6999999999 65533334788886 34654
No 165
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.90 E-value=13 Score=30.03 Aligned_cols=35 Identities=31% Similarity=0.797 Sum_probs=26.9
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCCC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHGE 334 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~~ 334 (561)
..||.|+..+. |.=+..=-...|-.|.+.|-+.|.
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWLDrGE 36 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWLDRGE 36 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEeecchh
Confidence 57999999988 666533456678899999987764
No 166
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.77 E-value=4.7 Score=44.82 Aligned_cols=31 Identities=35% Similarity=0.848 Sum_probs=25.4
Q ss_pred ccccccccccccC--CCeeeccCCCccccccce
Q 008581 140 ELTCGICFDTYSC--DKVVSAACGHPFCRACWR 170 (561)
Q Consensus 140 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~ 170 (561)
...|+||+..+-. -.++++.|||..|..|..
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~ 43 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQ 43 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHH
Confidence 4679999876532 467899999999999998
No 167
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=44.49 E-value=5.4 Score=30.68 Aligned_cols=24 Identities=38% Similarity=0.887 Sum_probs=17.4
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhh-hhhhcCc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFC-WLCLGAW 329 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FC-w~C~~~w 329 (561)
|-||.|+.+|.- ...|| -.|...|
T Consensus 4 kHC~~CG~~Ip~-------------~~~fCS~~C~~~~ 28 (59)
T PF09889_consen 4 KHCPVCGKPIPP-------------DESFCSPKCREEY 28 (59)
T ss_pred CcCCcCCCcCCc-------------chhhhCHHHHHHH
Confidence 789999999982 35566 4776554
No 168
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=44.26 E-value=11 Score=30.47 Aligned_cols=48 Identities=29% Similarity=0.734 Sum_probs=20.4
Q ss_pred CCccccccccccccC---CCeee--ccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 138 ARELTCGICFDTYSC---DKVVS--AACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~---~~~~~--l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
.....|.||-+.... .+++. ..|+-..|+.|+. +.+|. -.||+ |+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~----q~Cpq--Ckt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGN----QVCPQ--CKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-----SB-TT--T--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCc----ccccc--cCCCc
Confidence 345689999987643 23332 3488999999999 66663 46998 87543
No 169
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=44.13 E-value=14 Score=30.55 Aligned_cols=36 Identities=28% Similarity=0.697 Sum_probs=28.5
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
--||.|+.| ...|.-+.+. |+|.|=..|...|-.-.
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~--C~H~FH~hCI~kWl~~~ 68 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK--CSHNFHMHCILKWLSTQ 68 (85)
T ss_pred cCCCCccCC---CCCCceeecc--CccHHHHHHHHHHHccc
Confidence 468888887 3567777776 99999999999997543
No 170
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=43.44 E-value=19 Score=31.54 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=20.2
Q ss_pred CCCCCCCCcceee--cCCCCceEeCCCCcchh
Q 008581 292 SKPCPKCKRPIEK--NQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 292 tK~CP~C~~~IEK--~~GCnhm~C~~~C~~~F 321 (561)
.+-||+|+.++.- .++=+-+.|+ +|++++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~-kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCR-KCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECC-CCCcch
Confidence 3789999988775 1122378898 787764
No 171
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=43.42 E-value=17 Score=30.99 Aligned_cols=27 Identities=22% Similarity=0.582 Sum_probs=17.3
Q ss_pred CCCCCCCccee---ecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRPIE---KNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~IE---K~~GCnhm~C~~~C~~~ 320 (561)
-.||+|+.... +..|=-|..|. .||+.
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~-~CG~y 51 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCG-NCGLY 51 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECC-CCCCc
Confidence 58999993322 23355678887 67654
No 172
>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=43.41 E-value=11 Score=27.99 Aligned_cols=22 Identities=27% Similarity=0.708 Sum_probs=13.5
Q ss_pred ceeEe-cCCcccccccCcccCCC
Q 008581 244 FDVSC-LCSYNFCWNCTEEAHRP 265 (561)
Q Consensus 244 ~~v~C-~C~~~fC~~C~~~~H~p 265 (561)
....| .|+..||..|-.-.|..
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 45679 99999999998777754
No 173
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=43.23 E-value=5.1 Score=41.07 Aligned_cols=28 Identities=18% Similarity=0.427 Sum_probs=16.3
Q ss_pred CCCCCCCcceeec-CCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEKN-QGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK~-~GCnhm~C~~~C~~~F 321 (561)
.+||+|+..|-+. -.=|.+.|. .|+|+|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp-~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICE-QCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCC-CCCCCc
Confidence 6677777666542 334456665 566644
No 174
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.89 E-value=16 Score=42.32 Aligned_cols=35 Identities=23% Similarity=0.722 Sum_probs=29.2
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcch-----hhhhhhcC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFE-----FCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~-----FCw~C~~~ 328 (561)
-.||+|..++.-...=|.|.|. .||++ .|.-|+..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 4788888888766666889999 89988 89999876
No 175
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.32 E-value=12 Score=28.70 Aligned_cols=7 Identities=57% Similarity=1.644 Sum_probs=4.4
Q ss_pred CCCCCCC
Q 008581 293 KPCPKCK 299 (561)
Q Consensus 293 K~CP~C~ 299 (561)
-+||+|+
T Consensus 28 F~CPnCG 34 (61)
T COG2888 28 FPCPNCG 34 (61)
T ss_pred eeCCCCC
Confidence 3666666
No 176
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=42.25 E-value=3e+02 Score=27.30 Aligned_cols=23 Identities=35% Similarity=0.891 Sum_probs=16.8
Q ss_pred CCCCceEeCCCCc----chhhhhhhcCc
Q 008581 306 QGCMHMTCSPPCK----FEFCWLCLGAW 329 (561)
Q Consensus 306 ~GCnhm~C~~~C~----~~FCw~C~~~w 329 (561)
..|.||+|. +|- ..+|.+|....
T Consensus 21 TaC~HvfC~-~C~k~~~~~~C~lCkk~i 47 (233)
T KOG4739|consen 21 TACRHVFCE-PCLKASSPDVCPLCKKSI 47 (233)
T ss_pred eechhhhhh-hhcccCCcccccccccee
Confidence 469999987 554 45899998764
No 177
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=42.05 E-value=17 Score=26.77 Aligned_cols=26 Identities=19% Similarity=0.600 Sum_probs=14.0
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
+.||+|+--+.-..-=+...|. +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CG-kCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACG-KCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEec-cccc
Confidence 7889888533322111235666 5654
No 178
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.01 E-value=19 Score=36.60 Aligned_cols=27 Identities=41% Similarity=0.921 Sum_probs=20.7
Q ss_pred CCCCCCCCcceee--cCCCCceEeCCCCcc
Q 008581 292 SKPCPKCKRPIEK--NQGCMHMTCSPPCKF 319 (561)
Q Consensus 292 tK~CP~C~~~IEK--~~GCnhm~C~~~C~~ 319 (561)
-++||.|+.+|+| .+|=.--+|. .|+.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp-~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP-QCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC-CCcC
Confidence 3799999999997 3676667776 6764
No 179
>PF12773 DZR: Double zinc ribbon
Probab=41.50 E-value=13 Score=27.12 Aligned_cols=11 Identities=45% Similarity=1.186 Sum_probs=5.9
Q ss_pred CCCCCCCccee
Q 008581 293 KPCPKCKRPIE 303 (561)
Q Consensus 293 K~CP~C~~~IE 303 (561)
+.||+|+.++.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 45555555554
No 180
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=41.45 E-value=28 Score=24.28 Aligned_cols=21 Identities=38% Similarity=0.975 Sum_probs=13.0
Q ss_pred CCCCCCCcceee---cCCCCceEeC
Q 008581 293 KPCPKCKRPIEK---NQGCMHMTCS 314 (561)
Q Consensus 293 K~CP~C~~~IEK---~~GCnhm~C~ 314 (561)
+.||.|+..+.. ..| ..+.|+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECC
Confidence 579999866553 234 555665
No 181
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=41.35 E-value=56 Score=27.92 Aligned_cols=55 Identities=16% Similarity=0.191 Sum_probs=32.9
Q ss_pred CCCceecCCCCCCCe-eecccCCCCceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhH
Q 008581 220 NRKTKWCPAPGCEHA-IDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNC 279 (561)
Q Consensus 220 ~~~~~~CP~~~C~~~-i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~ 279 (561)
.+.+..||+ |+.. +......+...+.| .||+.+=.. ..+.-.+-+.|..|+....
T Consensus 18 lpt~f~CP~--Cge~~v~v~~~k~~~h~~C~~CG~y~~~~---V~~l~epIDVY~~wiD~~~ 74 (99)
T PRK14892 18 LPKIFECPR--CGKVSISVKIKKNIAIITCGNCGLYTEFE---VPSVYDEVDVYNKFIDLYL 74 (99)
T ss_pred CCcEeECCC--CCCeEeeeecCCCcceEECCCCCCccCEE---CCccccchhhHHHHHHHHH
Confidence 356788998 8733 32222234567789 898885332 2233334478899987654
No 182
>PRK12495 hypothetical protein; Provisional
Probab=41.13 E-value=19 Score=35.12 Aligned_cols=24 Identities=29% Similarity=0.819 Sum_probs=17.1
Q ss_pred CCCCCCCCcceeecCCCCceEeCCCCc
Q 008581 292 SKPCPKCKRPIEKNQGCMHMTCSPPCK 318 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm~C~~~C~ 318 (561)
.+.||.|+.||-+..|| .+|. .|+
T Consensus 42 a~hC~~CG~PIpa~pG~--~~Cp-~CQ 65 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ--EFCP-TCQ 65 (226)
T ss_pred hhhcccccCcccCCCCe--eECC-CCC
Confidence 47999999999966555 3454 444
No 183
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=40.92 E-value=5.5 Score=30.38 Aligned_cols=38 Identities=32% Similarity=0.744 Sum_probs=16.6
Q ss_pred CCCCCCCCcceeecCCCCce-EeCCCCcchhhhhhhcCccCCC
Q 008581 292 SKPCPKCKRPIEKNQGCMHM-TCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm-~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
+.+||.|+++++-..+=.+. +|+..|+ -+=|+.|...+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk----~iDLg~W~~e~ 40 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCK----LIDLGRWANEE 40 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHH----HHHHS-SSSSS
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhc----ccCHHHHhcCC
Confidence 36899999999954433332 5542222 12245676544
No 184
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=40.87 E-value=21 Score=36.35 Aligned_cols=27 Identities=37% Similarity=0.865 Sum_probs=20.9
Q ss_pred CCCCCCCCcceeec--CCCCceEeCCCCcc
Q 008581 292 SKPCPKCKRPIEKN--QGCMHMTCSPPCKF 319 (561)
Q Consensus 292 tK~CP~C~~~IEK~--~GCnhm~C~~~C~~ 319 (561)
-++||.|+.+|+|. +|=.-.+|. .|+.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCP-RCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECc-CCCC
Confidence 36999999999973 776667776 6763
No 185
>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=40.82 E-value=26 Score=22.57 Aligned_cols=21 Identities=24% Similarity=0.842 Sum_probs=14.0
Q ss_pred CCCCCCcceeecCCCCceEeC
Q 008581 294 PCPKCKRPIEKNQGCMHMTCS 314 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~ 314 (561)
.||.|+..+.+..|=-+.+|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999887788886
No 186
>smart00336 BBOX B-Box-type zinc finger.
Probab=40.73 E-value=23 Score=24.39 Aligned_cols=28 Identities=29% Similarity=0.640 Sum_probs=24.7
Q ss_pred CCCCCCC-cceeecCCCCceEeCCCCcchhhhhhhcC
Q 008581 293 KPCPKCK-RPIEKNQGCMHMTCSPPCKFEFCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~-~~IEK~~GCnhm~C~~~C~~~FCw~C~~~ 328 (561)
..|+.|. .++. ++|. .|....|..|...
T Consensus 4 ~~C~~h~~~~~~-------~~C~-~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCE-ECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceE-------EECC-CCCcccccccChh
Confidence 6799998 8888 9999 8999999999754
No 187
>PRK10220 hypothetical protein; Provisional
Probab=40.26 E-value=23 Score=30.58 Aligned_cols=27 Identities=30% Similarity=0.703 Sum_probs=16.4
Q ss_pred CCCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 292 SKPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
.-+||+|....-=..|=+ +.|. .|+|+
T Consensus 3 lP~CP~C~seytY~d~~~-~vCp-eC~hE 29 (111)
T PRK10220 3 LPHCPKCNSEYTYEDNGM-YICP-ECAHE 29 (111)
T ss_pred CCcCCCCCCcceEcCCCe-EECC-cccCc
Confidence 368999987655444432 5665 55554
No 188
>PRK11827 hypothetical protein; Provisional
Probab=40.01 E-value=23 Score=27.35 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=19.3
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
-.||.|+.+++-..+=+...|. .|+-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~-~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICK-LDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECC-ccCe
Confidence 5899999998866555667787 5543
No 189
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.69 E-value=22 Score=36.09 Aligned_cols=25 Identities=40% Similarity=0.915 Sum_probs=19.8
Q ss_pred CCCCCCCcceeec--CCCCceEeCCCCc
Q 008581 293 KPCPKCKRPIEKN--QGCMHMTCSPPCK 318 (561)
Q Consensus 293 K~CP~C~~~IEK~--~GCnhm~C~~~C~ 318 (561)
++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCP-QCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECC-CCC
Confidence 6999999999974 776667776 674
No 190
>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=39.25 E-value=86 Score=21.91 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=29.5
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChhhhhHhhh
Q 008581 79 EDDITKVSTVL-SISRVDASILLRHYNWSVSKVHDAWF 115 (561)
Q Consensus 79 ~~~i~~v~~vl-~i~~~~a~~LL~~~~W~~~~l~e~~~ 115 (561)
.+.|..+.+++ +++++.....|..+++|++..++...
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL 39 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALL 39 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 35677788877 57899999999999999999887654
No 191
>PRK10445 endonuclease VIII; Provisional
Probab=38.75 E-value=23 Score=35.76 Aligned_cols=26 Identities=27% Similarity=0.586 Sum_probs=20.8
Q ss_pred CCCCCCCCcceee--cCCCCceEeCCCCc
Q 008581 292 SKPCPKCKRPIEK--NQGCMHMTCSPPCK 318 (561)
Q Consensus 292 tK~CP~C~~~IEK--~~GCnhm~C~~~C~ 318 (561)
-++||.|+.+|++ .+|=.-.+|. .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP-~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCP-GCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECC-CCc
Confidence 3799999999997 4777777776 675
No 192
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.46 E-value=23 Score=35.96 Aligned_cols=26 Identities=35% Similarity=0.889 Sum_probs=20.1
Q ss_pred CCCCCCCCcceee--cCCCCceEeCCCCc
Q 008581 292 SKPCPKCKRPIEK--NQGCMHMTCSPPCK 318 (561)
Q Consensus 292 tK~CP~C~~~IEK--~~GCnhm~C~~~C~ 318 (561)
.++||+|+.+|++ .+|=.--+|. .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP-~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCP-HCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECc-CCc
Confidence 4799999999997 3676666776 675
No 193
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.15 E-value=13 Score=39.91 Aligned_cols=33 Identities=24% Similarity=0.649 Sum_probs=24.2
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDH 332 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h 332 (561)
-.||-|...+. +.+. . .|+|.||..|...|-..
T Consensus 27 l~C~IC~d~~~-----~Pvi-t-pCgH~FCs~CI~~~l~~ 59 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-T-SCSHTFCSLCIRRCLSN 59 (397)
T ss_pred cCCCcCchhhh-----CccC-C-CCCCchhHHHHHHHHhC
Confidence 68999987764 2332 4 69999999999876543
No 194
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.63 E-value=24 Score=36.00 Aligned_cols=26 Identities=42% Similarity=0.920 Sum_probs=20.9
Q ss_pred CCCCCCCCcceee--cCCCCceEeCCCCc
Q 008581 292 SKPCPKCKRPIEK--NQGCMHMTCSPPCK 318 (561)
Q Consensus 292 tK~CP~C~~~IEK--~~GCnhm~C~~~C~ 318 (561)
-++||.|+.+|+| .+|=.-.+|. .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCP-NCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECC-CCc
Confidence 3799999999997 4777777786 775
No 195
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.16 E-value=14 Score=40.24 Aligned_cols=28 Identities=29% Similarity=0.724 Sum_probs=18.5
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchhhhhhhc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLG 327 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~ 327 (561)
-.||-|-.+-. .-++..|||-|||-|+-
T Consensus 187 ~~CPICL~~~~-------~p~~t~CGHiFC~~CiL 214 (513)
T KOG2164|consen 187 MQCPICLEPPS-------VPVRTNCGHIFCGPCIL 214 (513)
T ss_pred CcCCcccCCCC-------cccccccCceeeHHHHH
Confidence 68999976655 33332477777777764
No 196
>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=37.00 E-value=1e+02 Score=24.01 Aligned_cols=40 Identities=13% Similarity=0.269 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhh
Q 008581 75 KCQQEDDITKVSTVLSISRVDASILLRHYNWSVSKVHDAW 114 (561)
Q Consensus 75 ~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~ 114 (561)
...+.+.|..++...++...-+..+|...+||-+..+..|
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3467888999999999999999999999999999988776
No 197
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=36.65 E-value=14 Score=28.19 Aligned_cols=40 Identities=30% Similarity=0.512 Sum_probs=30.5
Q ss_pred CCCCCCCcceee--cCCCCceEeCCCCcchhhhhhhcCccCCC
Q 008581 293 KPCPKCKRPIEK--NQGCMHMTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 293 K~CP~C~~~IEK--~~GCnhm~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
..||-|+...-- .+-=|+-+|. .|+...|-+||=.-.+|-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT-~Ck~~VCnlCGFNP~Phl 44 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCT-ECKSQVCNLCGFNPTPHL 44 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHH-HHhhhhhcccCCCCCccc
Confidence 579999987621 1346899999 899999999986555554
No 198
>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=36.47 E-value=20 Score=31.85 Aligned_cols=26 Identities=8% Similarity=0.043 Sum_probs=17.9
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
+.||+|++..---.- +.++|. .||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP-~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSP-YTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCC-CcCCc
Confidence 789999976653222 678887 67655
No 199
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=36.28 E-value=5.2 Score=29.42 Aligned_cols=32 Identities=22% Similarity=0.788 Sum_probs=26.6
Q ss_pred CccccccccccccCCCeee-ccCCCccccccce
Q 008581 139 RELTCGICFDTYSCDKVVS-AACGHPFCRACWR 170 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~ 170 (561)
..++|..|-+.+|..+... .-||.--|..||+
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~ 38 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQ 38 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhh
Confidence 3688999999888777655 4599999999998
No 200
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.10 E-value=20 Score=41.43 Aligned_cols=101 Identities=17% Similarity=0.291 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCh----hhhhHhhhcChH------------------HHHHHcCCCCCCccc
Q 008581 77 QQEDDITKVSTVLSISRVDASILLRHYNWSV----SKVHDAWFADED------------------AVRKSVGFLDKPVVE 134 (561)
Q Consensus 77 ~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~----~~l~e~~~~~~~------------------~~~~~~gl~~~~~~~ 134 (561)
...+.++.|-.---|||-...-+|.+..--. ...+-+|..+.+ +.+..++........
T Consensus 758 ~v~~vl~~I~~~~~ippl~VL~~Lakn~~ltls~IkD~ii~~l~~~~~~I~qd~~~Ie~yk~~i~e~r~~l~~lr~sa~i 837 (933)
T KOG2114|consen 758 IVYKVLEAIEMQERIPPLHVLQILAKNGTLTLSVIKDYIIKWLNKYSTIIEQDEDAIEVYKKDIEEKRQELETLRTSAQI 837 (933)
T ss_pred HHHHHHHHHHhcccCCHHHHHHHHhcCCceEEehhHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHHHHHHhhcccce
Confidence 4455555666666788888887776543221 112223333222 222222222211111
Q ss_pred cCCCCccccccccccccCCCeeeccCCCccccccceeccCCcccccccCCCCCCC
Q 008581 135 FSNARELTCGICFDTYSCDKVVSAACGHPFCRACWRVNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 135 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~i~~g~~~~~i~CP~~~C~~ 189 (561)
-..-.|..|--.+. -.+|...|||.|-..|+. ++ .-.||. |..
T Consensus 838 ---~q~skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--~~----~~~CP~--C~~ 880 (933)
T KOG2114|consen 838 ---FQVSKCSACEGTLD-LPFVHFLCGHSYHQHCLE--DK----EDKCPK--CLP 880 (933)
T ss_pred ---eeeeeecccCCccc-cceeeeecccHHHHHhhc--cC----cccCCc--cch
Confidence 11347999976652 244667899999999998 32 467987 876
No 201
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=35.62 E-value=11 Score=37.89 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=21.3
Q ss_pred CCCCCCCcceee-cCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKRPIEK-NQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~~IEK-~~GCnhm~C~~~C~~~F 321 (561)
.+||.|+..+-+ .-+=|...|. .|+|+|
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp-~c~~h~ 57 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCP-KCGHHM 57 (294)
T ss_pred eECCCccceeeHHHHHhhhhccc-ccCccc
Confidence 789999988875 3566777887 787665
No 202
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=35.38 E-value=8.3 Score=39.26 Aligned_cols=53 Identities=23% Similarity=0.663 Sum_probs=37.6
Q ss_pred CCCceecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCC
Q 008581 220 NRKTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKC 298 (561)
Q Consensus 220 ~~~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C 298 (561)
++.+-+|-. |+..|..- -+= .|.+.||..|... |. . |.||.|
T Consensus 87 ~p~VHfCd~--Cd~PI~IY-------GRmIPCkHvFCl~CAr~-~~------------------d---------K~Cp~C 129 (389)
T KOG2932|consen 87 GPRVHFCDR--CDFPIAIY-------GRMIPCKHVFCLECARS-DS------------------D---------KICPLC 129 (389)
T ss_pred CcceEeecc--cCCcceee-------ecccccchhhhhhhhhc-Cc------------------c---------ccCcCc
Confidence 455677776 88776432 122 6999999999743 21 1 999999
Q ss_pred CcceeecCCCC
Q 008581 299 KRPIEKNQGCM 309 (561)
Q Consensus 299 ~~~IEK~~GCn 309 (561)
.-.|+|.+-|+
T Consensus 130 ~d~VqrIeq~~ 140 (389)
T KOG2932|consen 130 DDRVQRIEQIM 140 (389)
T ss_pred ccHHHHHHHhc
Confidence 99999887764
No 203
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=34.71 E-value=46 Score=34.95 Aligned_cols=13 Identities=46% Similarity=0.938 Sum_probs=8.5
Q ss_pred ccCCCCCCCCCCc
Q 008581 7 DFYSGEAMDDDND 19 (561)
Q Consensus 7 ~~~~~~~~~~d~~ 19 (561)
.||-|..++++++
T Consensus 273 ~yftGea~d~~~~ 285 (337)
T PTZ00007 273 YWFLGEAIDEDSD 285 (337)
T ss_pred HhhCCCccccccc
Confidence 4788876665553
No 204
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=34.29 E-value=5.9e+02 Score=29.66 Aligned_cols=72 Identities=24% Similarity=0.328 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhhcccceecccCccchhhhhHHHHHHHHHHHhHHHHHHHHHHHHHHhhcccchhhHHHHHH
Q 008581 412 SQLKFIIDAWLQIVECRRVLKWTYAYGYYLPEHEHAKRQFFEYLQGEAESGLERLHQCAEKELLQFLNDESQSKEFNDFR 491 (561)
Q Consensus 412 ~~~~fl~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~~e~~~e~L~~~le~~~~~~~~~~~~~~~~~~~~ 491 (561)
.+...|..|+..+.+=-..|. .-|..+..-|..||..+ +++-+++|.+...|-+.- +++.++|
T Consensus 587 ~~~e~L~~aL~amqdk~~~LE------~sLsaEtriKldLfsaL-g~akrq~ei~~~~~~~~d----------~ei~~lk 649 (697)
T PF09726_consen 587 KDTEVLMSALSAMQDKNQHLE------NSLSAETRIKLDLFSAL-GDAKRQLEIAQGQLRKKD----------KEIEELK 649 (697)
T ss_pred hhHHHHHHHHHHHHHHHHHHH------HhhhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH----------HHHHHHH
Confidence 345555555555555444441 11122223356666665 566666666655443211 2344566
Q ss_pred HHHHHHHHH
Q 008581 492 TKLAGLTSV 500 (561)
Q Consensus 492 ~~~~~l~~~ 500 (561)
+||..+..|
T Consensus 650 ~ki~~~~av 658 (697)
T PF09726_consen 650 AKIAQLLAV 658 (697)
T ss_pred HHHHHHHhc
Confidence 666665544
No 205
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=34.26 E-value=27 Score=40.41 Aligned_cols=49 Identities=31% Similarity=0.560 Sum_probs=33.8
Q ss_pred CCccccccccccccCCCee-e-ccCCCccccccce-ecc---CCcccccccCCCCCC
Q 008581 138 ARELTCGICFDTYSCDKVV-S-AACGHPFCRACWR-VND---GPGCLMLRCPDPSCC 188 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~~~~~-~-l~CgH~fC~~C~~-i~~---g~~~~~i~CP~~~C~ 188 (561)
...++|.||++....+.++ + -.|-|.|-..||+ |.. ..+-...+||. |.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA--CQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc--cc
Confidence 4578999999987555443 3 3488999999999 421 11124689998 85
No 206
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=34.15 E-value=74 Score=27.25 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=16.7
Q ss_pred hhhhHHHHHHHHHHHhHHHHHHHHH
Q 008581 447 AKRQFFEYLQGEAESGLERLHQCAE 471 (561)
Q Consensus 447 ~~~~~fe~~Q~~~e~~~e~L~~~le 471 (561)
..+++++...+++|+....|...|+
T Consensus 75 e~k~~~~q~rK~~Ek~Aa~LT~~i~ 99 (101)
T PF09943_consen 75 EVKKVLRQVRKDLEKNAAKLTRKIE 99 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4466666667777777777766554
No 207
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=34.03 E-value=24 Score=24.75 Aligned_cols=31 Identities=29% Similarity=0.708 Sum_probs=18.6
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccC
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSD 331 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~ 331 (561)
.||+|+..++...- . .=....|-.|++.|-+
T Consensus 1 ~CP~C~~~l~~~~~-~------~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-G------DVEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE-C------CEEEEECCCCCeEEcc
Confidence 59999998875433 1 1222335567777754
No 208
>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=33.94 E-value=46 Score=24.69 Aligned_cols=36 Identities=11% Similarity=0.171 Sum_probs=30.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhh
Q 008581 80 DDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWF 115 (561)
Q Consensus 80 ~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~ 115 (561)
+.|..++...++.+.-+...|...+||-++.+..|.
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 568899999999999999999999999999888764
No 209
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=33.90 E-value=6.8 Score=41.08 Aligned_cols=47 Identities=26% Similarity=0.685 Sum_probs=34.9
Q ss_pred CccccccccccccC--CCeeeccCCCccccccce-eccCCcccccccCCCCCCC
Q 008581 139 RELTCGICFDTYSC--DKVVSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 139 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~ 189 (561)
-.+.|+.|-+.+.. .....+||.|.|-..|+. |-... .+-.||. |+.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n--~~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN--GTRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC--CCCCCcc--HHH
Confidence 36789999987643 455679999999999999 43322 2568998 873
No 210
>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=33.86 E-value=40 Score=30.14 Aligned_cols=37 Identities=35% Similarity=0.827 Sum_probs=17.3
Q ss_pred CCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCC--CCcceeecCCCCceEeCCCCcch
Q 008581 263 HRPVDCGTVAKWILKNCAESENMNWILANSKPCPK--CKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 263 H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~--C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
-+|+.|+...+ ...+ |+||+ |.-.++ ++-|+..||+-
T Consensus 68 lRPAicdkAR~----------KQq~-----k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 68 LRPAICDKARK----------KQQG-----KPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp E---SSHHHHH----------HHHH-----SB-SS--S--BEE------EE---TBTTB-
T ss_pred echHHhHHHHH----------HhcC-----CCCCccccCCcee------EEeccCcCCCc
Confidence 35778876543 1122 99999 999998 48898546553
No 211
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=33.04 E-value=47 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=10.5
Q ss_pred CCCCCCcc-eeecCCCCceEeC
Q 008581 294 PCPKCKRP-IEKNQGCMHMTCS 314 (561)
Q Consensus 294 ~CP~C~~~-IEK~~GCnhm~C~ 314 (561)
.||.|+.. |.-...=.-+.|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~ 23 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCP 23 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEET
T ss_pred CCcCCcCCceEEcCCCCeEECC
Confidence 58888764 2323233334555
No 212
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=32.98 E-value=34 Score=28.97 Aligned_cols=29 Identities=31% Similarity=0.823 Sum_probs=18.8
Q ss_pred eecCCCCCCCeeecccCCCCceeEe-cCCccc
Q 008581 224 KWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNF 254 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~f 254 (561)
.+||. |++.+.+..+.....+.| .|++.|
T Consensus 2 ~FCP~--Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCPT--CGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccCC--CCCEEEEecCCeEeeEEcCCCCcee
Confidence 47987 888887765544455566 665543
No 213
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=32.95 E-value=2.3e+02 Score=24.91 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=6.5
Q ss_pred CCCCCccee
Q 008581 295 CPKCKRPIE 303 (561)
Q Consensus 295 CP~C~~~IE 303 (561)
||.|+..+.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 888876655
No 214
>PRK11546 zraP zinc resistance protein; Provisional
Probab=32.81 E-value=3.9e+02 Score=24.47 Aligned_cols=55 Identities=11% Similarity=0.164 Sum_probs=39.0
Q ss_pred hhhhhHHHHHHHHHHHhHHHHHHHHHH---HHHHhhcccchh-hHHHHHHHHHHHHHHH
Q 008581 446 HAKRQFFEYLQGEAESGLERLHQCAEK---ELLQFLNDESQS-KEFNDFRTKLAGLTSV 500 (561)
Q Consensus 446 ~~~~~~fe~~Q~~~e~~~e~L~~~le~---~~~~~~~~~~~~-~~~~~~~~~~~~l~~~ 500 (561)
.++...++.+..+....++.|.+.|-. ||+.|+....|. +.+..+..+|.+|..-
T Consensus 46 ~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~k 104 (143)
T PRK11546 46 TEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQS 104 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 346777888888888888888886633 777787776665 3367777777776543
No 215
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.61 E-value=35 Score=22.92 Aligned_cols=27 Identities=26% Similarity=0.283 Sum_probs=15.1
Q ss_pred CCCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 292 SKPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
.+.|+.|+....-+.-=..++|. .|+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~-~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCI-FCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcc-cCCc
Confidence 37899888776633222334554 4443
No 216
>PF14149 YhfH: YhfH-like protein
Probab=32.52 E-value=3.9 Score=28.23 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=20.2
Q ss_pred CCCCCCCCcceeecCCCCceEeCCCC
Q 008581 292 SKPCPKCKRPIEKNQGCMHMTCSPPC 317 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm~C~~~C 317 (561)
.|.||.|+..|+-..-|-.+.|. .|
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~C~-~C 37 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNECD-RC 37 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCcCC-CC
Confidence 49999999999977777777776 45
No 217
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.47 E-value=22 Score=43.06 Aligned_cols=30 Identities=23% Similarity=0.571 Sum_probs=22.3
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcchh-----hhhhhcCc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFEF-----CWLCLGAW 329 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~F-----Cw~C~~~w 329 (561)
..||+|+..+.. -+|. .||... |-.|+...
T Consensus 668 rkCPkCG~~t~~------~fCP-~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCP-DCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCc-ccCCcCCCceeCccCCCcc
Confidence 789999987653 2887 788664 88887754
No 218
>PHA02664 hypothetical protein; Provisional
Probab=32.21 E-value=1.1e+02 Score=31.48 Aligned_cols=10 Identities=20% Similarity=0.272 Sum_probs=4.6
Q ss_pred HHHHHHHHHh
Q 008581 80 DDITKVSTVL 89 (561)
Q Consensus 80 ~~i~~v~~vl 89 (561)
+.+..|+++|
T Consensus 523 ~vl~ava~ml 532 (534)
T PHA02664 523 AVLGAVAEML 532 (534)
T ss_pred HHHHHHHHHh
Confidence 3344454444
No 219
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=32.18 E-value=3.6e+02 Score=23.87 Aligned_cols=24 Identities=17% Similarity=0.450 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 008581 485 KEFNDFRTKLAGLTSVTKNYFENL 508 (561)
Q Consensus 485 ~~~~~~~~~~~~l~~~~~~~~~~~ 508 (561)
+....+|.+|.++..+.+.....|
T Consensus 96 E~veEL~~Dv~DlK~myr~Qi~~l 119 (120)
T PF12325_consen 96 EEVEELRADVQDLKEMYREQIDQL 119 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456678888888877776655544
No 220
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=31.82 E-value=33 Score=32.77 Aligned_cols=25 Identities=28% Similarity=0.796 Sum_probs=20.3
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcch
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
.||+|+.++.+ .+.|+|.|. .|++.
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~-~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCP-NCGNI 175 (189)
T ss_pred EccccCCceEE-CCCCEEECC-CCCCE
Confidence 79999999987 455999998 78653
No 221
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=31.63 E-value=38 Score=24.34 Aligned_cols=24 Identities=25% Similarity=0.617 Sum_probs=10.3
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcc
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
.|..|+..++...+ .-+.|+ .||+
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~-~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCR-ECGY 27 (44)
T ss_pred ECCCCCCEeecCCC-CceECC-CCCc
Confidence 34555554443322 334444 4443
No 222
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.47 E-value=50 Score=24.94 Aligned_cols=28 Identities=25% Similarity=0.506 Sum_probs=20.4
Q ss_pred ecCCCCCCCeeecccCCCCceeEe-cCCccc
Q 008581 225 WCPAPGCEHAIDFAAGSGNFDVSC-LCSYNF 254 (561)
Q Consensus 225 ~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~f 254 (561)
-||. |+..|..........|.| .||..+
T Consensus 4 ~CP~--CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECPD--CGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCCC--CCCEEecCCCccCCEEeCCCCCCEE
Confidence 5886 999888765444456789 798775
No 223
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=30.70 E-value=32 Score=19.75 Aligned_cols=16 Identities=44% Similarity=0.960 Sum_probs=13.0
Q ss_pred cccccCcccCCCCCch
Q 008581 254 FCWNCTEEAHRPVDCG 269 (561)
Q Consensus 254 fC~~C~~~~H~p~~C~ 269 (561)
.|+.|++.-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5999999999877664
No 224
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.41 E-value=27 Score=35.70 Aligned_cols=29 Identities=34% Similarity=0.832 Sum_probs=21.6
Q ss_pred CCCCCCCcceeecCCCCceEeCC-CCcchhhhhhhcC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSP-PCKFEFCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~-~C~~~FCw~C~~~ 328 (561)
.-|-+|..+|- ++=+- .|+|.||+.|-..
T Consensus 91 HfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 91 HFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred EeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 57999999997 44441 4888888888654
No 225
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.40 E-value=7.2 Score=45.33 Aligned_cols=51 Identities=20% Similarity=0.462 Sum_probs=33.9
Q ss_pred CCccccccccccccC---CCe--eeccCCCccccccce-eccCCcccccccCCCCCCCcch
Q 008581 138 ARELTCGICFDTYSC---DKV--VSAACGHPFCRACWR-VNDGPGCLMLRCPDPSCCAAVG 192 (561)
Q Consensus 138 ~~~~~C~IC~e~~~~---~~~--~~l~CgH~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v~ 192 (561)
.+..+|+||+..... +-| ....|.|.|...|+- |-... ..-+||. |+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss--~~s~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS--ARSNCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc--CCCCCCc--cccccc
Confidence 456789999986542 112 123489999999998 54322 2568998 886654
No 226
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.14 E-value=40 Score=34.26 Aligned_cols=36 Identities=19% Similarity=0.553 Sum_probs=25.7
Q ss_pred hHHHHHhcCCCCCCCCcceeecCCCCceEeCCCCcchh
Q 008581 284 NMNWILANSKPCPKCKRPIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 284 ~~~wi~~ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~F 321 (561)
-..|...+ +-||+|+.+.+-..|=-.+.|. .|++.+
T Consensus 104 l~~w~~~~-RFCg~CG~~~~~~~~g~~~~C~-~cg~~~ 139 (279)
T COG2816 104 LLEWYRSH-RFCGRCGTKTYPREGGWARVCP-KCGHEH 139 (279)
T ss_pred HHHHHhhC-cCCCCCCCcCccccCceeeeCC-CCCCcc
Confidence 34564443 8999999998877776777777 677654
No 227
>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=29.93 E-value=34 Score=25.02 Aligned_cols=26 Identities=23% Similarity=0.627 Sum_probs=18.4
Q ss_pred CCCC--CCCcceeecCCCCceEeCCCCcc
Q 008581 293 KPCP--KCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP--~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
+.|| .|+.-+.-..--+-.+|. +|+.
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CG-KCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCG-KCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEET-TTSS
T ss_pred hcCCCcccCCceEeeecCCCccCC-Cccc
Confidence 7899 999877655556678888 7874
No 228
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.88 E-value=18 Score=32.44 Aligned_cols=51 Identities=25% Similarity=0.649 Sum_probs=35.9
Q ss_pred CCCccccccccccccCCCeee--ccCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 137 NARELTCGICFDTYSCDKVVS--AACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~--l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
+....+|.||-|......... --||-..|..|.. |.... ....||. |+..+
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~--~ypvCPv--CkTSF 131 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN--LYPVCPV--CKTSF 131 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc--cCCCCCc--ccccc
Confidence 346789999999753222221 1299999999988 65543 4678998 98765
No 229
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=29.74 E-value=33 Score=24.31 Aligned_cols=31 Identities=29% Similarity=0.749 Sum_probs=16.5
Q ss_pred cCCCCCCCeeecccCCCCceeEe-cCCcccccccCcc-cC
Q 008581 226 CPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEE-AH 263 (561)
Q Consensus 226 CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~-~H 263 (561)
|..++|..... ..+.| .|+..||..++.+ .|
T Consensus 1 C~~~~C~~~~~-------~~~~C~~C~~~FC~~Hr~~e~H 33 (43)
T PF01428_consen 1 CSFPGCKKKDF-------LPFKCKHCGKSFCLKHRLPEDH 33 (43)
T ss_dssp -SSTTT--BCT-------SHEE-TTTS-EE-TTTHSTTTC
T ss_pred CccCcCcCccC-------CCeECCCCCcccCccccCcccc
Confidence 44456764332 45789 7999999998754 35
No 230
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=29.35 E-value=57 Score=25.47 Aligned_cols=34 Identities=29% Similarity=0.499 Sum_probs=20.2
Q ss_pred CceecCCCCCCCeeecccCCCCceeEe-cCCccccc
Q 008581 222 KTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCW 256 (561)
Q Consensus 222 ~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 256 (561)
.++.||.-+|..+.... ..+-..+.| .|+...+.
T Consensus 5 ~lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA-ISGYYRAKCNGCESRTGY 39 (64)
T ss_pred cccCCCCCCCceeEEEe-cCceEEEEcCCCCcCccc
Confidence 46889995555443332 233455778 88886433
No 231
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.30 E-value=19 Score=41.78 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=26.8
Q ss_pred CccccccccccccCCCeeeccCCCccccccce
Q 008581 139 RELTCGICFDTYSCDKVVSAACGHPFCRACWR 170 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 170 (561)
+.-.|.+|.-.+-....+..+|||.|-.+|+.
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~ 847 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLI 847 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHH
Confidence 35679999987766666778999999999998
No 232
>PF07417 Crl: Transcriptional regulator Crl; InterPro: IPR009986 This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [].These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. They also stimulate RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.; GO: 0016987 sigma factor activity, 0045893 positive regulation of transcription, DNA-dependent, 0005737 cytoplasm; PDB: 3RPJ_A.
Probab=29.25 E-value=85 Score=27.86 Aligned_cols=47 Identities=23% Similarity=0.328 Sum_probs=28.4
Q ss_pred HhhcccceecccCccchhhhhHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 008581 430 VLKWTYAYGYYLPEHEHAKRQFFEYLQGEAESGLERLHQCAEKELLQ 476 (561)
Q Consensus 430 ~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~~e~~~e~L~~~le~~~~~ 476 (561)
...|.|-+|.|-...+=....|=...|.+++..++..|+.|..-|.+
T Consensus 64 ~F~y~Y~~Glydk~G~W~~~~i~~~~~~~v~~Tl~~Fh~kL~~~L~~ 110 (125)
T PF07417_consen 64 GFEYRYQFGLYDKEGNWQAEKIKKEVQEEVERTLRDFHQKLVELLEE 110 (125)
T ss_dssp EEEEEEEEEEE-TTS-EES----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEeeccccCCCCeeecCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888755432223444777778888888887777766655
No 233
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.20 E-value=7e+02 Score=27.99 Aligned_cols=15 Identities=27% Similarity=0.434 Sum_probs=7.0
Q ss_pred HHHHHHHHhcccccc
Q 008581 506 ENLVRALENGLADVD 520 (561)
Q Consensus 506 ~~~~~~~e~~l~~~~ 520 (561)
...+++|.+|+.-++
T Consensus 668 ~~~~~~L~~~iET~~ 682 (741)
T KOG4460|consen 668 PDQLRHLGNAIETVT 682 (741)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444555554444
No 234
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.58 E-value=31 Score=26.00 Aligned_cols=31 Identities=32% Similarity=0.984 Sum_probs=24.7
Q ss_pred cccccccccccc-CCCeeecc-CCCccccccce
Q 008581 140 ELTCGICFDTYS-CDKVVSAA-CGHPFCRACWR 170 (561)
Q Consensus 140 ~~~C~IC~e~~~-~~~~~~l~-CgH~fC~~C~~ 170 (561)
...|++|-+.+. .++++.-+ ||-.|-++||.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 456999998874 56676655 99999999997
No 235
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=28.53 E-value=36 Score=25.98 Aligned_cols=23 Identities=30% Similarity=0.857 Sum_probs=16.3
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
+.-.||+|+.+.. .|-.|. .||+
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~-~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCP-SCGY 48 (57)
T ss_pred cceECCCCCCccC-----CeEECC-CCCc
Confidence 3468999999887 366665 5653
No 236
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=28.24 E-value=33 Score=36.27 Aligned_cols=34 Identities=29% Similarity=0.778 Sum_probs=27.2
Q ss_pred CCCccccccccccccCCCeeeccCCCccccccce
Q 008581 137 NARELTCGICFDTYSCDKVVSAACGHPFCRACWR 170 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 170 (561)
+.....|+|||-.+|...-..--|.-..|..|+.
T Consensus 71 ~rr~~ecpicflyyps~~n~~rcC~~~Ic~ecf~ 104 (482)
T KOG2789|consen 71 SRRKTECPICFLYYPSAKNLVRCCSETICGECFA 104 (482)
T ss_pred ccccccCceeeeecccccchhhhhccchhhhhee
Confidence 3456899999998876555556799999999988
No 237
>PHA02325 hypothetical protein
Probab=28.23 E-value=27 Score=27.08 Aligned_cols=13 Identities=38% Similarity=0.792 Sum_probs=9.8
Q ss_pred cCCCCCCCCccee
Q 008581 291 NSKPCPKCKRPIE 303 (561)
Q Consensus 291 ntK~CP~C~~~IE 303 (561)
++|.||+|+..--
T Consensus 2 ~~k~CPkC~A~Wl 14 (72)
T PHA02325 2 DTKICPKCGARWL 14 (72)
T ss_pred CccccCccCCEeE
Confidence 4689999987543
No 238
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.14 E-value=26 Score=31.34 Aligned_cols=37 Identities=35% Similarity=0.750 Sum_probs=25.3
Q ss_pred CCCCCCcceeecCCCCceEeCCCCcchhhhhhhcCccCCC
Q 008581 294 PCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGAWSDHG 333 (561)
Q Consensus 294 ~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~w~~h~ 333 (561)
.|--|.+.- =..||.| .|. -|...||-.|++...--.
T Consensus 67 tC~IC~KTK-FADG~GH-~C~-YCq~r~CARCGGrv~lrs 103 (169)
T KOG3799|consen 67 TCGICHKTK-FADGCGH-NCS-YCQTRFCARCGGRVSLRS 103 (169)
T ss_pred chhhhhhcc-cccccCc-ccc-hhhhhHHHhcCCeeeecc
Confidence 444444321 1589999 466 699999999998655443
No 239
>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=28.06 E-value=41 Score=33.34 Aligned_cols=36 Identities=28% Similarity=0.768 Sum_probs=0.0
Q ss_pred hHHHHHhcCCCCCCCCcc-eee---cCCCCceEeCCCCcchh
Q 008581 284 NMNWILANSKPCPKCKRP-IEK---NQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 284 ~~~wi~~ntK~CP~C~~~-IEK---~~GCnhm~C~~~C~~~F 321 (561)
+..|+..|. .||+|+.. +.+ |.-=--..|. .|+.+|
T Consensus 24 tE~Wv~~n~-yCP~Cg~~~L~~f~NN~PVaDF~C~-~C~eey 63 (254)
T PF06044_consen 24 TEDWVAENM-YCPNCGSKPLSKFENNRPVADFYCP-NCNEEY 63 (254)
T ss_dssp HHHHHHHH----TTT--SS-EE--------EEE-T-TT--EE
T ss_pred HHHHHHHCC-cCCCCCChhHhhccCCCccceeECC-CCchHH
No 240
>PLN02189 cellulose synthase
Probab=27.97 E-value=35 Score=40.78 Aligned_cols=47 Identities=32% Similarity=0.849 Sum_probs=33.4
Q ss_pred CccccccccccccC---CCe-eecc-CCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 139 RELTCGICFDTYSC---DKV-VSAA-CGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 139 ~~~~C~IC~e~~~~---~~~-~~l~-CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
....|.||.+.... .++ +... |+-..|+.|.. ..+| .-.||+ |+...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg----~q~Cpq--Ckt~Y 86 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREG----TQNCPQ--CKTRY 86 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC----CccCcc--cCCch
Confidence 34589999998542 223 3444 88999999999 4555 457999 88754
No 241
>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=27.87 E-value=42 Score=26.13 Aligned_cols=34 Identities=24% Similarity=0.565 Sum_probs=16.8
Q ss_pred CCCccccccccccccCCCe--eeccCCCccccccce
Q 008581 137 NARELTCGICFDTYSCDKV--VSAACGHPFCRACWR 170 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~C~~ 170 (561)
+.....|.+|...|....- .--.||+.||..|..
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhC
Confidence 3446779999988743211 224599999999998
No 242
>cd07620 BAR_SH3BP1 The Bin/Amphiphysin/Rvs (BAR) domain of SH3-domain Binding Protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. SH3-domain binding protein 1 (SH3BP1 or 3BP-1) is a Rac GTPase activating protein that inhibits Rac-mediated platelet-derived growth factor (PDGF)-induced membrane ruffling. SH3BP1 contains an N-terminal BAR domain followed by a GAP domain for Rho and Rac GTPases and a C-terminal proline-rich domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=27.81 E-value=6.4e+02 Score=25.42 Aligned_cols=112 Identities=15% Similarity=0.207 Sum_probs=69.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhhcccceecccCc--------------------cchhhhhHHHHHHHHHHHhHHHHHHHHH
Q 008581 412 SQLKFIIDAWLQIVECRRVLKWTYAYGYYLPE--------------------HEHAKRQFFEYLQGEAESGLERLHQCAE 471 (561)
Q Consensus 412 ~~~~fl~~a~~~l~~~r~~L~~sy~~~yy~~~--------------------~~~~~~~~fe~~Q~~~e~~~e~L~~~le 471 (561)
.++.-|...-+.|.. ++|=|.|+..=|... ....|.++....+.+++..+|.=.+.++
T Consensus 118 ~dL~~I~k~rKkL~k--~~LD~D~~K~R~~~a~k~s~~~~~~~~~~~~~~~~~~~~K~~~lkeE~eea~~K~E~~kd~~~ 195 (257)
T cd07620 118 EDLPEILKNKKQFAK--LTTDWNSAKSRSPQAAGRSPRSGGRSEEVGEHQGIRRANKGEPLKEEEEECWRKLEQCKDQYS 195 (257)
T ss_pred hhHHHHHHHHHHHHh--HHhhHHHHHHHHHHhhccccCCccccccccccccccccccccccHHHHHHHHHHHHHHHHHHH
Confidence 455555555555554 456666666433100 0124455777778888888888888888
Q ss_pred HHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccc
Q 008581 472 KELLQFLNDESQSKEFNDFRTKLAGLTSVTKNYFENLVRALENGLADVDSHAACSKTTNS 531 (561)
Q Consensus 472 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~~ 531 (561)
.++-.|+..+.. +=..+..+...-..|.+.=+..|+.-+|.+.-+-..+.++.+
T Consensus 196 a~Mynfl~kE~e------~a~~l~~lveaQ~~YHrqsl~~Le~~l~~~~~~~~~~~~~~~ 249 (257)
T cd07620 196 ADLYHFATKEDS------YANYFIRLLELQAEYHKNSLEFLDKNITELKENHSQKEPSVS 249 (257)
T ss_pred HHHHHHHHhhHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcc
Confidence 888777765432 222245555556678888888899889988755444444433
No 243
>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=27.58 E-value=1.9e+02 Score=20.16 Aligned_cols=38 Identities=8% Similarity=0.184 Sum_probs=29.8
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChhhhhHhhhc
Q 008581 79 EDDITKVSTVL-SISRVDASILLRHYNWSVSKVHDAWFA 116 (561)
Q Consensus 79 ~~~i~~v~~vl-~i~~~~a~~LL~~~~W~~~~l~e~~~~ 116 (561)
.+.|..+.+++ +++++.++..|..+++|++..++....
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 34566777776 568889999999999999998876543
No 244
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.52 E-value=1e+02 Score=36.56 Aligned_cols=33 Identities=18% Similarity=0.164 Sum_probs=18.1
Q ss_pred ecHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcC
Q 008581 69 LREADIKCQQEDDITKVSTVLSISRVDASILLRHYN 104 (561)
Q Consensus 69 lt~~~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~ 104 (561)
|.+-|......+.+..++. -++.....|+++..
T Consensus 955 LD~VD~f~~f~~~i~~lq~---~d~~~yq~l~~~L~ 987 (1010)
T KOG1991|consen 955 LDQVDPFQLFKEAITNLQS---SDAVRYQKLISTLT 987 (1010)
T ss_pred ccccchHHHHHHHHHhhhc---cChHHHHHHHhcCC
Confidence 5666666666666655543 33444555555433
No 245
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.27 E-value=27 Score=26.48 Aligned_cols=22 Identities=36% Similarity=0.869 Sum_probs=15.3
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCc
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCK 318 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~ 318 (561)
+.-.||.|+.+.. .|..|. .||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~-~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCP-SCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCT-TTB
T ss_pred ceeeeccCCCEec-----ccEeeC-CCC
Confidence 4468999998776 466665 565
No 246
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=27.04 E-value=45 Score=28.70 Aligned_cols=24 Identities=33% Similarity=1.003 Sum_probs=15.6
Q ss_pred CCCCCCCcce-eecCCCCceEeCCCCcc
Q 008581 293 KPCPKCKRPI-EKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP~C~~~I-EK~~GCnhm~C~~~C~~ 319 (561)
-+||+|+.-. -..++ +|.|. .|.+
T Consensus 4 p~cp~c~sEytYed~~--~~~cp-ec~~ 28 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICP-ECAH 28 (112)
T ss_pred CCCCccCCceEEecCc--eEeCc-hhcc
Confidence 6899996543 34455 77887 5544
No 247
>PRK01343 zinc-binding protein; Provisional
Probab=26.44 E-value=27 Score=26.67 Aligned_cols=12 Identities=42% Similarity=1.412 Sum_probs=10.4
Q ss_pred CCCCCCCCccee
Q 008581 292 SKPCPKCKRPIE 303 (561)
Q Consensus 292 tK~CP~C~~~IE 303 (561)
++.||.|+++..
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 489999999876
No 248
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.40 E-value=34 Score=40.33 Aligned_cols=25 Identities=36% Similarity=1.031 Sum_probs=20.1
Q ss_pred CCCCCCCc-ceeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKR-PIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~-~IEK~~GCnhm~C~~~C~~~ 320 (561)
-.||-|+. .||..|||| +|. .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~-~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCT-NCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--ccc-chhhh
Confidence 48999974 688899998 688 78765
No 249
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.28 E-value=42 Score=30.82 Aligned_cols=93 Identities=16% Similarity=0.213 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhHhhhcChHHHHHHcCCCCCCccccCC----CCccccccccc
Q 008581 73 DIKCQQEDDITKVSTVLSISRVDASILLRHYNWSVSKVHDAWFADEDAVRKSVGFLDKPVVEFSN----ARELTCGICFD 148 (561)
Q Consensus 73 ~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~----~~~~~C~IC~e 148 (561)
-....+.++|.+.-..+++...... +-..--|+.+.+.++ -.+.+...||.++.....+. .....||-|-.
T Consensus 39 pa~e~L~~~I~~aL~~~Gv~~V~V~-i~~~p~Wt~d~it~~----gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s 113 (146)
T TIGR02159 39 PALEVIRQDIRDAVRALGVEVVEVS-TSLDPPWTTDWITED----AREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGS 113 (146)
T ss_pred chHHHHHHHHHHHHHhcCCCeEEEe-EeeCCCCChHHCCHH----HHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCC
Confidence 3444444444443333466432222 334567888876653 12345677886543221111 12478999986
Q ss_pred ccc--CCCeeeccCC-Cccccccce
Q 008581 149 TYS--CDKVVSAACG-HPFCRACWR 170 (561)
Q Consensus 149 ~~~--~~~~~~l~Cg-H~fC~~C~~ 170 (561)
... .+.+-+..|. .++|.+|.+
T Consensus 114 ~~t~~~s~fg~t~cka~~~c~~c~e 138 (146)
T TIGR02159 114 ADTTITSIFGPTACKALYRCRACKE 138 (146)
T ss_pred CCcEeecCCCChhhHHHhhhhhhCC
Confidence 541 1233346686 467888876
No 250
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.16 E-value=40 Score=25.49 Aligned_cols=23 Identities=26% Similarity=0.675 Sum_probs=15.8
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
+.-.||+|+.+.. .|-.|. .||+
T Consensus 25 ~l~~C~~cG~~~~-----~H~vc~-~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKL-----PHRVCP-SCGY 47 (55)
T ss_pred cceECCCCCCccc-----CeeECC-ccCe
Confidence 3467999998877 566665 5653
No 251
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=25.95 E-value=23 Score=41.32 Aligned_cols=15 Identities=27% Similarity=0.341 Sum_probs=0.0
Q ss_pred CCCHHHHH-HHHHHcC
Q 008581 90 SISRVDAS-ILLRHYN 104 (561)
Q Consensus 90 ~i~~~~a~-~LL~~~~ 104 (561)
+|+.++|. +-.|-|.
T Consensus 721 Gi~eerAaria~RAfP 736 (787)
T PF03115_consen 721 GIPEERAARIAKRAFP 736 (787)
T ss_dssp ----------------
T ss_pred CCCHHHHHhhhhccCC
Confidence 56666443 4445444
No 252
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.79 E-value=45 Score=31.79 Aligned_cols=24 Identities=25% Similarity=0.739 Sum_probs=17.7
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcc
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~ 319 (561)
-.|++|+.++++ .=+.|+|. .|++
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp-~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCP-NCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECC-CCCC
Confidence 378888888888 44667887 6764
No 253
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=25.51 E-value=58 Score=24.64 Aligned_cols=29 Identities=31% Similarity=0.550 Sum_probs=15.1
Q ss_pred CceecCCCCCCCeeecccCC-CC-----ceeEe-cCCc
Q 008581 222 KTKWCPAPGCEHAIDFAAGS-GN-----FDVSC-LCSY 252 (561)
Q Consensus 222 ~~~~CP~~~C~~~i~~~~~~-~~-----~~v~C-~C~~ 252 (561)
.++.||. |+......... .. ..|.| .||.
T Consensus 2 ~LkPCPF--CG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPF--CGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCC--CCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678998 65443322111 11 45677 6766
No 254
>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=25.27 E-value=63 Score=24.82 Aligned_cols=27 Identities=22% Similarity=0.672 Sum_probs=19.0
Q ss_pred CCCCCCCcc----eeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRP----IEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~----IEK~~GCnhm~C~~~C~~~ 320 (561)
-.||+|+.. +-+..|=.++-|. .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv-~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECV-ECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-cCCCc
Confidence 379999864 3345666788998 78764
No 255
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=25.21 E-value=41 Score=22.49 Aligned_cols=9 Identities=33% Similarity=1.003 Sum_probs=3.7
Q ss_pred CCCCCccee
Q 008581 295 CPKCKRPIE 303 (561)
Q Consensus 295 CP~C~~~IE 303 (561)
|..|+..++
T Consensus 3 C~~Cg~~~~ 11 (32)
T PF03604_consen 3 CGECGAEVE 11 (32)
T ss_dssp ESSSSSSE-
T ss_pred CCcCCCeeE
Confidence 444444444
No 256
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.13 E-value=53 Score=39.46 Aligned_cols=47 Identities=32% Similarity=0.777 Sum_probs=33.4
Q ss_pred CccccccccccccCC---Ce-eec-cCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 139 RELTCGICFDTYSCD---KV-VSA-ACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 139 ~~~~C~IC~e~~~~~---~~-~~l-~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
....|.||-|+...+ ++ +.. .|+-..|+.|.. ..+| .-.||+ |+...
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG----~q~CPq--CktrY 69 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDG----NQSCPQ--CKTKY 69 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcC----CccCCc--cCCch
Confidence 345899999986432 33 333 489999999999 5555 457999 88754
No 257
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.88 E-value=3e+02 Score=29.46 Aligned_cols=23 Identities=39% Similarity=0.977 Sum_probs=13.2
Q ss_pred CCCCCCCc-ceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKR-PIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~-~IEK~~GCnhm~C~~~C~~~F 321 (561)
+-||+|+. -.| | -|.|. +||+.|
T Consensus 2 ~fC~kcG~qk~E---d--~~qC~-qCG~~~ 25 (465)
T COG4640 2 KFCPKCGSQKAE---D--DVQCT-QCGHKF 25 (465)
T ss_pred Cccccccccccc---c--ccccc-ccCCcC
Confidence 67899884 333 2 24576 665543
No 258
>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=24.39 E-value=39 Score=33.26 Aligned_cols=54 Identities=22% Similarity=0.384 Sum_probs=32.3
Q ss_pred ccccCCCCCCCcc-hhhHHhhhCChHHHHHHHHHHHHHHHhcCCCceecCCCCCCCeee
Q 008581 179 MLRCPDPSCCAAV-GQDMIDMLASDEDKKKYSRYLLRSYVEDNRKTKWCPAPGCEHAID 236 (561)
Q Consensus 179 ~i~CP~~~C~~~v-~~~~i~~ll~~e~~~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~ 236 (561)
.-+||. |+.-. ....++-+++++-+.+.-..-...... .....||.++|+.++.
T Consensus 10 d~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIFs--~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIFS--RGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHhc--CCCCCCCCccHHHHHH
Confidence 457998 77632 233455677777665544333333222 3346899999997765
No 259
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=24.36 E-value=84 Score=35.98 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=19.3
Q ss_pred CCCcchhhHHhhhCChHHHHHHHHHHHHHHHhc
Q 008581 187 CCAAVGQDMIDMLASDEDKKKYSRYLLRSYVED 219 (561)
Q Consensus 187 C~~~v~~~~i~~ll~~e~~~ky~~~l~~~~v~~ 219 (561)
|...+-.-.....++....++|..+.++-|...
T Consensus 1076 CSKAfmkLe~~e~l~~a~kq~ye~La~~iFsk~ 1108 (1189)
T KOG2041|consen 1076 CSKAFMKLEAFEELDDAEKQEYENLAFRIFSKN 1108 (1189)
T ss_pred hHHHHHHHHhhhhCCHHHHHHHHHHHHHHhccC
Confidence 444333222333456677888888877766543
No 260
>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=24.36 E-value=44 Score=29.33 Aligned_cols=36 Identities=22% Similarity=0.502 Sum_probs=26.5
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcC
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGA 328 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~ 328 (561)
+.+.|..|+.+.-...+.. ..|. .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~-~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCV-DCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEET-TTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCC-cCCccccCccCCc
Confidence 4578999998765555555 7888 8999999999875
No 261
>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=24.12 E-value=50 Score=36.74 Aligned_cols=35 Identities=20% Similarity=0.568 Sum_probs=22.7
Q ss_pred CCCCCCCcceeecCCCCceEeCCCCcch-----hhhhhhcC
Q 008581 293 KPCPKCKRPIEKNQGCMHMTCSPPCKFE-----FCWLCLGA 328 (561)
Q Consensus 293 K~CP~C~~~IEK~~GCnhm~C~~~C~~~-----FCw~C~~~ 328 (561)
-.||+|..++.--..=|.+.|. .||+. .|..|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCH-YCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcC-CCcCcCCCCCCCCCCCCC
Confidence 3677777666533333467887 78866 57778663
No 262
>PF07058 Myosin_HC-like: Myosin II heavy chain-like; InterPro: IPR009768 This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.
Probab=23.92 E-value=8.2e+02 Score=25.32 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHhcccccccc
Q 008581 501 TKNYFENLVRALENGLADVDSH 522 (561)
Q Consensus 501 ~~~~~~~~~~~~e~~l~~~~~~ 522 (561)
++..+...++.||+||-...+.
T Consensus 144 LkeK~klRLK~LEe~Lk~~~s~ 165 (351)
T PF07058_consen 144 LKEKLKLRLKVLEEGLKGSSSN 165 (351)
T ss_pred HHHHHHHHHHHHHhhccCCCCC
Confidence 3455677889999999876653
No 263
>PLN02436 cellulose synthase A
Probab=23.88 E-value=53 Score=39.42 Aligned_cols=47 Identities=32% Similarity=0.785 Sum_probs=33.3
Q ss_pred CccccccccccccC---CCe-eec-cCCCccccccce--eccCCcccccccCCCCCCCcc
Q 008581 139 RELTCGICFDTYSC---DKV-VSA-ACGHPFCRACWR--VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 139 ~~~~C~IC~e~~~~---~~~-~~l-~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~~v 191 (561)
....|.||-|+... .++ +.. .|+-..|+.|.. ..+| .-.||+ |+...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg----~~~Cpq--ckt~Y 88 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREG----NQACPQ--CKTRY 88 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC----CccCcc--cCCch
Confidence 34589999998632 233 333 388899999999 4555 457999 88754
No 264
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=23.82 E-value=16 Score=35.94 Aligned_cols=39 Identities=28% Similarity=0.812 Sum_probs=26.6
Q ss_pred eecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCch
Q 008581 224 KWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCG 269 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~ 269 (561)
.-||.|.|.....+. ..+.| .|+..||.+.+.+. ..+|.
T Consensus 99 ~kc~~~~c~k~~~~~-----~~~~c~~c~~~~c~khr~~~--dhsc~ 138 (250)
T KOG3183|consen 99 NKCPVPRCKKTLTLA-----NKITCSKCGRNFCLKHRHPL--DHSCN 138 (250)
T ss_pred ccCCchhhHHHHHHH-----HhhhhHhhcchhhhhccCCC--Cchhh
Confidence 468988887554332 35789 99999999977432 23565
No 265
>PF14353 CpXC: CpXC protein
Probab=23.80 E-value=49 Score=29.31 Aligned_cols=46 Identities=22% Similarity=0.491 Sum_probs=25.7
Q ss_pred cccCCCCCCCcchhhHH---hhhCChHHHHHHHHHHHHHHHhcCCCceecCCCCCCCeeec
Q 008581 180 LRCPDPSCCAAVGQDMI---DMLASDEDKKKYSRYLLRSYVEDNRKTKWCPAPGCEHAIDF 237 (561)
Q Consensus 180 i~CP~~~C~~~v~~~~i---~~ll~~e~~~ky~~~l~~~~v~~~~~~~~CP~~~C~~~i~~ 237 (561)
+.||. |+..+..+.. ..-..+++.++ .++..-....||. |+..+..
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP~--Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCPS--CGHKFRL 50 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECCC--CCCceec
Confidence 68998 8887754433 22233343332 2223334578887 8766654
No 266
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.75 E-value=34 Score=26.55 Aligned_cols=12 Identities=42% Similarity=1.262 Sum_probs=10.2
Q ss_pred CCCCCCCCccee
Q 008581 292 SKPCPKCKRPIE 303 (561)
Q Consensus 292 tK~CP~C~~~IE 303 (561)
+.+||.|+++++
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 368999999986
No 267
>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=23.74 E-value=33 Score=25.50 Aligned_cols=26 Identities=23% Similarity=0.685 Sum_probs=14.1
Q ss_pred CCCCCCCcceeecCCC--CceEeCCCCcc
Q 008581 293 KPCPKCKRPIEKNQGC--MHMTCSPPCKF 319 (561)
Q Consensus 293 K~CP~C~~~IEK~~GC--nhm~C~~~C~~ 319 (561)
-+|++|++.+-+.++= -.+.|. .|+.
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCp-RC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCP-RCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECC-CCCc
Confidence 4677776666654322 236665 5543
No 268
>KOG0219 consensus Mismatch repair ATPase MSH2 (MutS family) [Replication, recombination and repair]
Probab=23.31 E-value=1.2e+03 Score=27.60 Aligned_cols=29 Identities=21% Similarity=0.376 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008581 484 SKEFNDFRTKLAGLTSVTKNYFENLVRAL 512 (561)
Q Consensus 484 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 512 (561)
.+++.++|++|..|...+..-.......|
T Consensus 458 deeL~eLrq~LdeL~~~m~~~hkrv~~dl 486 (902)
T KOG0219|consen 458 DEELQELREKLDELERKMEKLHKKVSADL 486 (902)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 37789999999998877665544444433
No 269
>COG0021 TktA Transketolase [Carbohydrate transport and metabolism]
Probab=23.28 E-value=3.9e+02 Score=30.60 Aligned_cols=98 Identities=20% Similarity=0.303 Sum_probs=53.3
Q ss_pred HHHHHHHHHhhcccceecccCccchhhhhHHHH---HHHHHHHhHHHHHHHHH-------HHHHHhhcccchhhHHHHHH
Q 008581 422 LQIVECRRVLKWTYAYGYYLPEHEHAKRQFFEY---LQGEAESGLERLHQCAE-------KELLQFLNDESQSKEFNDFR 491 (561)
Q Consensus 422 ~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~---~Q~~~e~~~e~L~~~le-------~~~~~~~~~~~~~~~~~~~~ 491 (561)
+.+...|..|-|.|.- ||+++. ....|+. ....++..-+.+-..-+ .++...+..+.|. .+..+.
T Consensus 270 ~ev~~~k~~lgw~~~~-F~vp~e---v~~~~~~~~~~g~~~~~~W~~~~~~y~~~~Pe~~~~~~r~~~~~~p~-~~~~~~ 344 (663)
T COG0021 270 EEVAAAKKALGWEPEP-FEVPEE---VYAAFRAVEERGAKAEAAWNELFAAYKKKYPELAAEFERRLNGELPA-NWAAFL 344 (663)
T ss_pred HHHHHHHHHhCCCCCc-eecCHH---HHHHHHHHhhhhhhHHHHHHHHHHHHHhhChHHHHHHHHHhcccCch-hHHHhh
Confidence 4577888999999998 998654 3333432 22233333332222211 1222233333331 122221
Q ss_pred HHHH--HHHHHHHHHHHHHHHHHHhcccccccccc
Q 008581 492 TKLA--GLTSVTKNYFENLVRALENGLADVDSHAA 524 (561)
Q Consensus 492 ~~~~--~l~~~~~~~~~~~~~~~e~~l~~~~~~~~ 524 (561)
.++. .....||++..+.+++|-.-||++---.+
T Consensus 345 ~~~~~~~~~~ATR~as~~~L~~l~~~~p~l~GGSA 379 (663)
T COG0021 345 PKFEANGKSIATRKASGKALNALAKKLPELIGGSA 379 (663)
T ss_pred hhhcccccccchHHHHHHHHHHHHhhCccccccCc
Confidence 1221 22357899999999999999999864333
No 270
>PLN03184 chloroplast Hsp70; Provisional
Probab=23.00 E-value=1.2e+03 Score=27.05 Aligned_cols=19 Identities=11% Similarity=0.130 Sum_probs=12.9
Q ss_pred EecHHHHHHHHHHHHHHHH
Q 008581 68 VLREADIKCQQEDDITKVS 86 (561)
Q Consensus 68 vlt~~~i~~~~~~~i~~v~ 86 (561)
.+++++|...+-..+.+.+
T Consensus 146 ~~speei~a~iL~~lk~~a 164 (673)
T PLN03184 146 QFAAEEISAQVLRKLVDDA 164 (673)
T ss_pred EEcHHHHHHHHHHHHHHHH
Confidence 5778888777766665543
No 271
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=22.93 E-value=38 Score=27.78 Aligned_cols=28 Identities=32% Similarity=0.759 Sum_probs=14.3
Q ss_pred CCCCCCCc------ceeecCCCCceEeCCCCcchh
Q 008581 293 KPCPKCKR------PIEKNQGCMHMTCSPPCKFEF 321 (561)
Q Consensus 293 K~CP~C~~------~IEK~~GCnhm~C~~~C~~~F 321 (561)
-.||.|+. -|.|..|=.++.|+ .|+..|
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~-~Cg~~~ 56 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCR-VCGESF 56 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEES-SS--EE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEec-CCCCeE
Confidence 58999982 23345677778888 675443
No 272
>PLN02189 cellulose synthase
Probab=22.72 E-value=63 Score=38.73 Aligned_cols=60 Identities=27% Similarity=0.722 Sum_probs=39.4
Q ss_pred eecCCCCCCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCCCcce
Q 008581 224 KWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKCKRPI 302 (561)
Q Consensus 224 ~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C~~~I 302 (561)
.-|.- |+-.|... ..+..-|-| .|++-.|..|-+- .. .+ .++.||+|+...
T Consensus 35 ~~C~i--Cgd~vg~~-~~g~~fvaC~~C~fpvCr~Cyey----------er------~e---------g~q~CpqCkt~Y 86 (1040)
T PLN02189 35 QVCEI--CGDEIGLT-VDGDLFVACNECGFPVCRPCYEY----------ER------RE---------GTQNCPQCKTRY 86 (1040)
T ss_pred ccccc--cccccCcC-CCCCEEEeeccCCCccccchhhh----------hh------hc---------CCccCcccCCch
Confidence 35665 77666543 345677899 8999999988621 10 11 127899999888
Q ss_pred eecCCCCce
Q 008581 303 EKNQGCMHM 311 (561)
Q Consensus 303 EK~~GCnhm 311 (561)
.+--||+.+
T Consensus 87 ~r~kgs~~v 95 (1040)
T PLN02189 87 KRLKGSPRV 95 (1040)
T ss_pred hhccCCCCc
Confidence 866666653
No 273
>KOG2662 consensus Magnesium transporters: CorA family [Inorganic ion transport and metabolism]
Probab=22.48 E-value=3.8e+02 Score=28.79 Aligned_cols=42 Identities=17% Similarity=0.263 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cccccccccccc
Q 008581 485 KEFNDFRTKLAGLTSVTKNYFENLVRALEN--GLADVDSHAACS 526 (561)
Q Consensus 485 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~--~l~~~~~~~~~~ 526 (561)
..+..++.+|..+++-++...+.+-.-|++ +|.++-.+...+
T Consensus 220 ~~lr~~k~~Lt~l~~rvqkvRDeLe~LLddd~Dma~mYLT~K~~ 263 (414)
T KOG2662|consen 220 ERLRILKKRLTELTSRVQKVRDELEELLDDDDDMAEMYLTRKLA 263 (414)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHhHHhh
Confidence 455566666776666666555555555543 466666555543
No 274
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.48 E-value=38 Score=40.23 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=21.6
Q ss_pred cCCCCCCCCcceeecCCCCceEeCCCCcc-----hhhhhhhc
Q 008581 291 NSKPCPKCKRPIEKNQGCMHMTCSPPCKF-----EFCWLCLG 327 (561)
Q Consensus 291 ntK~CP~C~~~IEK~~GCnhm~C~~~C~~-----~FCw~C~~ 327 (561)
..+.||.|+... ..-.|. .||. .||-.|+.
T Consensus 625 g~RfCpsCG~~t------~~frCP-~CG~~Te~i~fCP~CG~ 659 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCP-FCGTHTEPVYRCPRCGI 659 (1121)
T ss_pred cCccCCCCCCcC------CcccCC-CCCCCCCcceeCccccC
Confidence 458899998874 336787 7885 48888854
No 275
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.41 E-value=1.3e+02 Score=21.59 Aligned_cols=28 Identities=18% Similarity=0.477 Sum_probs=16.6
Q ss_pred cCCCCCCCCcc-eeecCCCCceEeCCCCcc
Q 008581 291 NSKPCPKCKRP-IEKNQGCMHMTCSPPCKF 319 (561)
Q Consensus 291 ntK~CP~C~~~-IEK~~GCnhm~C~~~C~~ 319 (561)
+.-.||+|+.. +-+..+=....|. .|++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~-~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCK-ACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECC-CCCC
Confidence 34579999974 2233344445666 5664
No 276
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=22.36 E-value=1.1e+02 Score=34.99 Aligned_cols=34 Identities=18% Similarity=0.469 Sum_probs=21.4
Q ss_pred CceecCCCCCCCeeecccCCCCceeEe-cCCcccccccC
Q 008581 222 KTKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNFCWNCT 259 (561)
Q Consensus 222 ~~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~ 259 (561)
.++||-.-+|..+|.. ..+-|.= .=|--||.+|-
T Consensus 21 PLVYCDG~nCsVAVHQ----aCYGIvqVPtGpWfCrKCe 55 (900)
T KOG0956|consen 21 PLVYCDGHNCSVAVHQ----ACYGIVQVPTGPWFCRKCE 55 (900)
T ss_pred ceeeecCCCceeeeeh----hcceeEecCCCchhhhhhh
Confidence 4689999999988863 2333322 34555666665
No 277
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.34 E-value=58 Score=39.15 Aligned_cols=55 Identities=24% Similarity=0.716 Sum_probs=35.7
Q ss_pred CCCeeecccCCCCceeEe-cCCcccccccCcccCCCCCchhHHHHHHHhHhhhHhHHHHHhcCCCCCCCCcceeecCCCC
Q 008581 231 CEHAIDFAAGSGNFDVSC-LCSYNFCWNCTEEAHRPVDCGTVAKWILKNCAESENMNWILANSKPCPKCKRPIEKNQGCM 309 (561)
Q Consensus 231 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~~~~~wi~~ntK~CP~C~~~IEK~~GCn 309 (561)
|+--|-.. ..+..-|-| .|++-.|..|-+ +.. .+ .++-||+|+....+--||.
T Consensus 23 CGD~vg~~-~~Ge~FVAC~eC~FPVCrpCYE----------YEr------~e---------G~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 23 CGDNVGKT-VDGEPFVACDVCAFPVCRPCYE----------YER------KD---------GNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred cccccCcC-CCCCEEEEeccCCCccccchhh----------hhh------hc---------CCccCCccCCchhhhcCCC
Confidence 66555444 346677899 999999988762 211 11 1278999888887666665
Q ss_pred ce
Q 008581 310 HM 311 (561)
Q Consensus 310 hm 311 (561)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 53
No 278
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=22.05 E-value=41 Score=34.17 Aligned_cols=46 Identities=24% Similarity=0.624 Sum_probs=33.0
Q ss_pred CCCccccccccccccC--CCeeeccCCCccccccce--eccCCcccccccCCCCCCC
Q 008581 137 NARELTCGICFDTYSC--DKVVSAACGHPFCRACWR--VNDGPGCLMLRCPDPSCCA 189 (561)
Q Consensus 137 ~~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~--i~~g~~~~~i~CP~~~C~~ 189 (561)
....+.||||.+..-. ..+..++|||.--..|++ +.. .+.||. |..
T Consensus 155 ~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-----~y~CP~--C~~ 204 (276)
T KOG1940|consen 155 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-----GYTCPI--CSK 204 (276)
T ss_pred hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-----CCCCCc--ccc
Confidence 3446679999986432 344568999988888888 332 388998 877
No 279
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=21.93 E-value=75 Score=25.39 Aligned_cols=27 Identities=26% Similarity=0.764 Sum_probs=18.9
Q ss_pred CCCCCCCcc----eeecCCCCceEeCCCCcch
Q 008581 293 KPCPKCKRP----IEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 293 K~CP~C~~~----IEK~~GCnhm~C~~~C~~~ 320 (561)
-.||+|+.. +-+..|=.++.|. .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV-~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECV-ECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-CCCCe
Confidence 379999865 2244667788998 78653
No 280
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.87 E-value=76 Score=27.76 Aligned_cols=30 Identities=20% Similarity=0.573 Sum_probs=20.4
Q ss_pred ceecCCCCCCCeeecccCCCCceeEe-cCCccc
Q 008581 223 TKWCPAPGCEHAIDFAAGSGNFDVSC-LCSYNF 254 (561)
Q Consensus 223 ~~~CP~~~C~~~i~~~~~~~~~~v~C-~C~~~f 254 (561)
+.+||. |+..+............| .||+.+
T Consensus 2 m~FCp~--Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPK--CGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCC--ccCeeEEeEcCCCcEEECCCCCcch
Confidence 468997 998887653333346678 788764
No 281
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=21.81 E-value=1.2e+03 Score=26.65 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Q 008581 486 EFNDFRTKLAGLTSVTKNYFENLVRALENGLAD 518 (561)
Q Consensus 486 ~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~ 518 (561)
....+++++..|..+.......+...-..|+|.
T Consensus 590 ~~~~~~~kl~eL~~~~~pi~~r~~~~~~~~~~~ 622 (653)
T PTZ00009 590 EKEEFEHKQKEVESVCNPIMTKMYQAAGGGMPG 622 (653)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCC
Confidence 445677778877777776555554444445553
No 282
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.79 E-value=43 Score=26.08 Aligned_cols=13 Identities=38% Similarity=1.152 Sum_probs=11.5
Q ss_pred CCCCCCCCcceee
Q 008581 292 SKPCPKCKRPIEK 304 (561)
Q Consensus 292 tK~CP~C~~~IEK 304 (561)
+.+||.|+++++.
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5799999999985
No 283
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=21.71 E-value=5.6e+02 Score=28.46 Aligned_cols=38 Identities=16% Similarity=0.145 Sum_probs=28.3
Q ss_pred HHhhhHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 008581 367 SLEKYTHYYERWASNQSSRQKALADLHQMQTVHLEKLS 404 (561)
Q Consensus 367 ~l~ry~~y~~r~~~h~~s~~~~~~~l~~~~~~~~~~l~ 404 (561)
..+||..|-+++..|+.-++++...|+.+++.+++...
T Consensus 408 ~~~~l~~lt~~~~~~ee~l~~Lt~~l~~l~~~~i~~~~ 445 (543)
T COG1315 408 IVERLKELTEEISLHEERLKKLTKLLVALVKVKIESKK 445 (543)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45677888888999999888888888877765444443
No 284
>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=20.87 E-value=8.1e+02 Score=24.09 Aligned_cols=60 Identities=28% Similarity=0.376 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 008581 452 FEYLQGEAESGLERLHQCAEKELLQFLNDESQSKEFNDFRTKLAGLTSVTKNYFENLVRALENGL 516 (561)
Q Consensus 452 fe~~Q~~~e~~~e~L~~~le~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l 516 (561)
-|..|.+++...|.++..+.+|+..|-. ....+||.-|+.+.-.--.+.+..+.-|.+-|
T Consensus 156 AE~~~~~a~~~Fe~iS~~~k~El~rF~~-----~Rv~~fk~~lve~aE~~ik~Ak~~~~~l~~~~ 215 (219)
T cd07621 156 AEAAQQEACEKFESMSESAKQELLDFKT-----RRVAAFRKNLVELAELEIKHAKAQIQLLKNCL 215 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667889999999999999999887755 45667777777766555555555555554433
No 285
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=20.73 E-value=25 Score=25.75 Aligned_cols=44 Identities=23% Similarity=0.534 Sum_probs=20.2
Q ss_pred cccccccccccCCCeeeccC-CCccccccceeccCCcccccccCCCCCCCcchh
Q 008581 141 LTCGICFDTYSCDKVVSAAC-GHPFCRACWRVNDGPGCLMLRCPDPSCCAAVGQ 193 (561)
Q Consensus 141 ~~C~IC~e~~~~~~~~~l~C-gH~fC~~C~~i~~g~~~~~i~CP~~~C~~~v~~ 193 (561)
+.|--|+-.. .. .+.| .|+.|..|+.+--+. .-.||. |+.++|.
T Consensus 3 ~nCKsCWf~~--k~--Li~C~dHYLCl~CLt~ml~~---s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN--KG--LIKCSDHYLCLNCLTLMLSR---SDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S----SS--EEE-SS-EEEHHHHHHT-SS---SSEETT--TTEE---
T ss_pred ccChhhhhcC--CC--eeeecchhHHHHHHHHHhcc---ccCCCc--ccCcCcc
Confidence 5677787432 22 2456 489999999922221 346888 8887764
No 286
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.55 E-value=44 Score=26.62 Aligned_cols=42 Identities=26% Similarity=0.664 Sum_probs=28.4
Q ss_pred ccccccccccCCCeeeccCC--Cccccccce-eccCCcccccccCCCCCCCcc
Q 008581 142 TCGICFDTYSCDKVVSAACG--HPFCRACWR-VNDGPGCLMLRCPDPSCCAAV 191 (561)
Q Consensus 142 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~-i~~g~~~~~i~CP~~~C~~~v 191 (561)
.|..|-.++|....-.+-|. |.||.+|.. .-.| .||. |+..+
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g------~CPn--CGGel 51 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLHG------LCPN--CGGEL 51 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC------cCCC--CCchh
Confidence 47777777766655555563 789999988 3333 4887 87654
No 287
>PF06705 SF-assemblin: SF-assemblin/beta giardin
Probab=20.40 E-value=8.4e+02 Score=24.10 Aligned_cols=16 Identities=6% Similarity=0.366 Sum_probs=6.5
Q ss_pred hhHHHHHHHhhhHHHH
Q 008581 370 KYTHYYERWASNQSSR 385 (561)
Q Consensus 370 ry~~y~~r~~~h~~s~ 385 (561)
++.-|+..+......+
T Consensus 13 ~~~~f~~~le~e~~~R 28 (247)
T PF06705_consen 13 RFSGFESDLENEKRQR 28 (247)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444444433333
No 288
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.38 E-value=70 Score=32.21 Aligned_cols=34 Identities=18% Similarity=0.509 Sum_probs=24.1
Q ss_pred HHHHHhcCCCCCCCCcceeecCCCCceEeCCCCcch
Q 008581 285 MNWILANSKPCPKCKRPIEKNQGCMHMTCSPPCKFE 320 (561)
Q Consensus 285 ~~wi~~ntK~CP~C~~~IEK~~GCnhm~C~~~C~~~ 320 (561)
..|- .+.+-||.|+.++....+=..+.|. .|+..
T Consensus 93 ~~w~-~~~~fC~~CG~~~~~~~~~~~~~C~-~c~~~ 126 (256)
T PRK00241 93 AEFY-RSHRFCGYCGHPMHPSKTEWAMLCP-HCRER 126 (256)
T ss_pred HHHh-hcCccccccCCCCeecCCceeEECC-CCCCE
Confidence 3452 3468999999998876555668887 78743
No 289
>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=20.34 E-value=1.4e+03 Score=26.61 Aligned_cols=22 Identities=18% Similarity=0.170 Sum_probs=10.4
Q ss_pred hhhHHHHHHHHHHHhHHHHHHH
Q 008581 448 KRQFFEYLQGEAESGLERLHQC 469 (561)
Q Consensus 448 ~~~~fe~~Q~~~e~~~e~L~~~ 469 (561)
...+|.++-.++...++.|...
T Consensus 270 W~~vFr~l~~q~~~m~esver~ 291 (683)
T PF08580_consen 270 WNIVFRNLGRQAQKMCESVERS 291 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555554444444433
No 290
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.29 E-value=42 Score=33.85 Aligned_cols=31 Identities=23% Similarity=0.814 Sum_probs=20.5
Q ss_pred CCCCCCCCcceeecCCCCceEeCCCCcchhhhhhhcC
Q 008581 292 SKPCPKCKRPIEKNQGCMHMTCSPPCKFEFCWLCLGA 328 (561)
Q Consensus 292 tK~CP~C~~~IEK~~GCnhm~C~~~C~~~FCw~C~~~ 328 (561)
++.||.|+.+=- +.|+=. +|+|-+||.|...
T Consensus 239 ~~~C~~Cg~~Pt-----iP~~~~-~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPT-----IPHVIG-KCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCC-----CCeeec-cccceeehhhhhh
Confidence 579999986532 112222 4888899999763
No 291
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.18 E-value=1.3e+02 Score=22.92 Aligned_cols=34 Identities=15% Similarity=0.231 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhhH
Q 008581 79 EDDITKVSTVLSISRVDASILLRHYNWSVSKVHD 112 (561)
Q Consensus 79 ~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e 112 (561)
-..+.+|++.|++|+.....=...++|+...-++
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~~ 46 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKWDELLPIE 46 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCccccCchh
Confidence 4457899999999999999999999999765443
No 292
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=20.12 E-value=95 Score=30.14 Aligned_cols=70 Identities=26% Similarity=0.663 Sum_probs=39.6
Q ss_pred ccccccccccccCCCeeeccCCCc-cccccce---eccC-CcccccccCCCCCCCcchhhHHhhhCChHHHHHHHHHHHH
Q 008581 140 ELTCGICFDTYSCDKVVSAACGHP-FCRACWR---VNDG-PGCLMLRCPDPSCCAAVGQDMIDMLASDEDKKKYSRYLLR 214 (561)
Q Consensus 140 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~---i~~g-~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~~ky~~~l~~ 214 (561)
..+|-+|......+ .-.=.|. -|..|=+ |... ++..-++|| |+..+ +-
T Consensus 80 mvtCRVCq~~i~~e---gk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP---CNCLL--------IC------------- 132 (275)
T KOG4684|consen 80 MVTCRVCQVAISLE---GKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP---CNCLL--------IC------------- 132 (275)
T ss_pred eEeehhhhHHhccc---cccceeeEeecccCccccCCCCCCCCceeecC---CcEEE--------EE-------------
Confidence 67899997554221 1111231 3555655 6543 344578999 43322 00
Q ss_pred HHHhcCCCceecCCCCCCCeeeccc
Q 008581 215 SYVEDNRKTKWCPAPGCEHAIDFAA 239 (561)
Q Consensus 215 ~~v~~~~~~~~CP~~~C~~~i~~~~ 239 (561)
.......-||.|+|.++|...+
T Consensus 133 ---K~sSqRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 133 ---KASSQRIACPRPNCKRIINLDP 154 (275)
T ss_pred ---ecccceeccCCCCcceeeecCC
Confidence 1123456899999999997653
No 293
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.09 E-value=78 Score=19.77 Aligned_cols=7 Identities=57% Similarity=1.644 Sum_probs=4.5
Q ss_pred CCCCCCC
Q 008581 293 KPCPKCK 299 (561)
Q Consensus 293 K~CP~C~ 299 (561)
-+||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4677765
Done!