Query 009562
Match_columns 532
No_of_seqs 405 out of 1628
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 14:37:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009562.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009562hhsearch_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 7.5E-65 1.6E-69 544.6 23.6 410 1-438 20-436 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 2.6E-34 5.6E-39 301.4 10.6 267 10-305 85-374 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 1.1E-33 2.4E-38 286.1 11.7 205 56-265 182-416 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.9E-24 4.1E-29 211.7 8.3 197 55-260 218-442 (446)
5 smart00647 IBR In Between Ring 99.2 3.6E-11 7.8E-16 94.4 5.9 62 132-194 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 3.5E-11 7.7E-16 94.3 1.0 62 132-194 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 1.4E-08 3.1E-13 73.1 2.2 41 61-107 1-41 (42)
8 PF13923 zf-C3HC4_2: Zinc fing 98.2 6.7E-07 1.4E-11 63.3 2.5 37 61-107 1-38 (39)
9 PF00097 zf-C3HC4: Zinc finger 98.2 1.1E-06 2.4E-11 62.7 3.1 39 61-107 1-40 (41)
10 PF13639 zf-RING_2: Ring finge 98.2 9.1E-07 2E-11 64.3 2.3 40 60-107 2-42 (44)
11 PLN03208 E3 ubiquitin-protein 98.1 2.4E-06 5.1E-11 81.1 3.9 66 55-124 15-88 (193)
12 KOG0320 Predicted E3 ubiquitin 98.1 2E-06 4.3E-11 79.7 2.9 55 55-119 128-182 (187)
13 PF13445 zf-RING_UBOX: RING-ty 98.0 4E-06 8.7E-11 60.6 2.6 41 61-106 1-43 (43)
14 smart00647 IBR In Between Ring 97.9 1.9E-05 4.2E-10 61.6 5.0 37 217-253 17-58 (64)
15 PF13920 zf-C3HC4_3: Zinc fing 97.8 1.3E-05 2.8E-10 59.8 3.2 46 58-115 2-48 (50)
16 PF01485 IBR: IBR domain; Int 97.8 9E-06 1.9E-10 63.4 1.8 37 217-253 17-58 (64)
17 cd00162 RING RING-finger (Real 97.8 2E-05 4.4E-10 56.2 3.4 43 60-113 1-44 (45)
18 PF14634 zf-RING_5: zinc-RING 97.8 1.7E-05 3.8E-10 57.6 2.5 42 60-111 1-43 (44)
19 KOG0823 Predicted E3 ubiquitin 97.7 1.9E-05 4.2E-10 76.3 2.0 59 56-123 45-103 (230)
20 smart00504 Ubox Modified RING 97.6 4.8E-05 1E-09 59.2 3.7 48 59-118 2-49 (63)
21 KOG4367 Predicted Zn-finger pr 97.6 0.00037 7.9E-09 72.5 10.9 76 169-252 174-252 (699)
22 KOG2164 Predicted E3 ubiquitin 97.6 2.2E-05 4.7E-10 83.6 2.1 60 58-124 186-245 (513)
23 smart00184 RING Ring finger. E 97.6 5E-05 1.1E-09 52.2 2.7 38 61-107 1-38 (39)
24 KOG0317 Predicted E3 ubiquitin 97.5 4.3E-05 9.4E-10 76.0 2.1 52 56-119 237-288 (293)
25 PHA02926 zinc finger-like prot 97.5 7.7E-05 1.7E-09 71.8 3.0 56 55-114 167-229 (242)
26 TIGR00599 rad18 DNA repair pro 97.4 9.9E-05 2.1E-09 78.0 3.5 66 56-136 24-90 (397)
27 KOG2177 Predicted E3 ubiquitin 97.4 8.3E-05 1.8E-09 74.7 2.7 45 56-112 11-55 (386)
28 PHA02929 N1R/p28-like protein; 97.4 0.00013 2.8E-09 72.1 3.3 50 56-115 172-227 (238)
29 KOG0287 Postreplication repair 97.2 0.00025 5.5E-09 71.7 3.4 64 56-135 21-86 (442)
30 KOG0804 Cytoplasmic Zn-finger 96.8 0.42 9.2E-06 50.8 22.9 46 56-113 173-220 (493)
31 TIGR00570 cdk7 CDK-activating 96.7 0.0011 2.5E-08 67.5 3.1 54 59-121 4-60 (309)
32 KOG0978 E3 ubiquitin ligase in 96.6 0.00062 1.3E-08 76.0 0.5 55 57-122 642-696 (698)
33 PF11789 zf-Nse: Zinc-finger o 96.5 0.0019 4E-08 49.7 2.5 47 57-111 10-57 (57)
34 PF04564 U-box: U-box domain; 96.4 0.0021 4.5E-08 52.0 2.3 50 57-117 3-52 (73)
35 PF14835 zf-RING_6: zf-RING of 96.2 0.00078 1.7E-08 52.5 -1.0 43 58-114 7-50 (65)
36 COG5540 RING-finger-containing 96.0 0.005 1.1E-07 61.8 2.9 52 56-116 321-373 (374)
37 KOG1002 Nucleotide excision re 95.9 0.0034 7.4E-08 67.0 1.8 55 56-117 534-588 (791)
38 COG5574 PEX10 RING-finger-cont 95.9 0.0047 1E-07 61.1 2.5 53 57-119 214-266 (271)
39 KOG4628 Predicted E3 ubiquitin 95.9 0.0045 9.8E-08 64.2 2.3 45 59-112 230-275 (348)
40 PF14555 UBA_4: UBA-like domai 95.7 0.0089 1.9E-07 43.1 2.7 33 1-33 8-40 (43)
41 PF12678 zf-rbx1: RING-H2 zinc 95.6 0.0075 1.6E-07 48.8 2.3 41 59-107 20-71 (73)
42 COG5432 RAD18 RING-finger-cont 95.0 0.014 3.1E-07 58.2 2.3 49 56-116 23-71 (391)
43 KOG2879 Predicted E3 ubiquitin 94.9 0.024 5.3E-07 56.4 3.5 51 55-115 236-287 (298)
44 PF11793 FANCL_C: FANCL C-term 94.5 0.018 3.9E-07 46.2 1.3 57 58-116 2-67 (70)
45 KOG0824 Predicted E3 ubiquitin 94.3 0.024 5.2E-07 57.1 2.1 54 56-120 5-58 (324)
46 KOG4159 Predicted E3 ubiquitin 94.1 0.068 1.5E-06 56.9 5.1 49 56-116 82-130 (398)
47 PF14570 zf-RING_4: RING/Ubox 93.3 0.063 1.4E-06 39.7 2.2 44 61-113 1-46 (48)
48 KOG1812 Predicted E3 ubiquitin 93.1 0.082 1.8E-06 56.4 3.7 138 5-191 201-344 (384)
49 COG5243 HRD1 HRD ubiquitin lig 93.1 0.07 1.5E-06 55.2 3.0 49 56-114 285-344 (491)
50 COG5152 Uncharacterized conser 93.0 0.034 7.4E-07 52.6 0.6 32 57-90 195-226 (259)
51 KOG0311 Predicted E3 ubiquitin 92.6 0.026 5.5E-07 58.1 -1.0 49 56-114 41-89 (381)
52 KOG1428 Inhibitor of type V ad 92.4 0.21 4.5E-06 59.4 5.7 66 57-124 3485-3553(3738)
53 KOG0006 E3 ubiquitin-protein l 92.1 0.4 8.6E-06 48.7 6.8 147 13-192 285-439 (446)
54 KOG2660 Locus-specific chromos 92.0 0.1 2.2E-06 53.5 2.5 46 57-114 14-60 (331)
55 KOG1039 Predicted E3 ubiquitin 92.0 0.1 2.2E-06 54.5 2.6 56 55-113 158-219 (344)
56 KOG1814 Predicted E3 ubiquitin 91.1 0.24 5.3E-06 52.0 4.2 38 216-253 271-311 (445)
57 KOG0802 E3 ubiquitin ligase [P 91.0 0.23 4.9E-06 55.5 4.3 45 58-112 291-338 (543)
58 KOG4185 Predicted E3 ubiquitin 90.7 0.32 6.9E-06 49.9 4.7 56 58-122 3-64 (296)
59 KOG1645 RING-finger-containing 90.7 0.17 3.7E-06 53.1 2.6 49 58-114 4-55 (463)
60 PRK00420 hypothetical protein; 90.5 2.1 4.6E-05 37.5 8.9 27 218-252 23-49 (112)
61 PF10571 UPF0547: Uncharacteri 89.8 0.15 3.3E-06 32.8 0.9 23 219-245 1-24 (26)
62 PF12861 zf-Apc11: Anaphase-pr 89.6 0.3 6.5E-06 40.6 2.7 31 77-114 51-81 (85)
63 KOG4692 Predicted E3 ubiquitin 89.5 0.23 4.9E-06 51.2 2.3 52 53-116 417-468 (489)
64 TIGR00570 cdk7 CDK-activating 89.1 10 0.00022 39.2 13.9 52 151-231 5-56 (309)
65 KOG1734 Predicted RING-contain 88.7 0.23 5.1E-06 49.4 1.8 53 57-117 223-283 (328)
66 smart00744 RINGv The RING-vari 88.6 0.42 9.1E-06 35.5 2.7 42 60-107 1-47 (49)
67 PF05883 Baculo_RING: Baculovi 88.3 0.2 4.3E-06 45.1 1.0 34 58-91 26-66 (134)
68 KOG4265 Predicted E3 ubiquitin 87.4 0.52 1.1E-05 48.9 3.4 48 56-115 288-336 (349)
69 KOG0826 Predicted E3 ubiquitin 87.1 0.93 2E-05 46.5 4.9 49 56-114 298-347 (357)
70 KOG0828 Predicted E3 ubiquitin 85.7 0.41 8.9E-06 51.4 1.7 51 56-115 569-634 (636)
71 COG5220 TFB3 Cdk activating ki 85.5 0.22 4.8E-06 48.6 -0.3 49 59-114 11-63 (314)
72 KOG1785 Tyrosine kinase negati 83.9 0.52 1.1E-05 49.3 1.4 45 59-111 370-414 (563)
73 KOG1001 Helicase-like transcri 83.9 0.46 1E-05 54.2 1.2 48 59-117 455-502 (674)
74 KOG4172 Predicted E3 ubiquitin 83.8 0.38 8.2E-06 36.3 0.3 45 59-114 8-53 (62)
75 KOG0825 PHD Zn-finger protein 82.7 0.87 1.9E-05 51.5 2.6 39 58-96 96-139 (1134)
76 smart00661 RPOL9 RNA polymeras 81.9 1.2 2.7E-05 32.9 2.5 27 219-245 1-30 (52)
77 KOG1813 Predicted E3 ubiquitin 80.7 0.64 1.4E-05 47.0 0.7 45 58-114 241-285 (313)
78 KOG4739 Uncharacterized protei 80.3 0.48 1.1E-05 46.7 -0.3 45 59-115 4-48 (233)
79 PHA00626 hypothetical protein 79.8 1.4 3.1E-05 33.5 2.1 28 220-247 2-35 (59)
80 PF04641 Rtf2: Rtf2 RING-finge 79.3 1.5 3.3E-05 44.2 2.9 59 55-124 110-170 (260)
81 KOG1815 Predicted E3 ubiquitin 79.0 1.2 2.7E-05 48.4 2.3 46 218-271 158-206 (444)
82 PF10168 Nup88: Nuclear pore c 78.6 55 0.0012 38.0 15.5 48 374-422 601-648 (717)
83 KOG3039 Uncharacterized conser 77.8 1.3 2.9E-05 43.6 1.9 54 56-119 219-274 (303)
84 KOG0827 Predicted E3 ubiquitin 77.4 0.95 2.1E-05 47.4 0.8 49 58-113 4-54 (465)
85 KOG0823 Predicted E3 ubiquitin 77.2 1.3 2.7E-05 43.5 1.5 47 157-229 49-95 (230)
86 KOG0297 TNF receptor-associate 77.0 1.1 2.5E-05 47.9 1.3 47 55-113 18-65 (391)
87 KOG2817 Predicted E3 ubiquitin 76.0 2.2 4.8E-05 44.9 3.0 57 57-120 333-390 (394)
88 PF14952 zf-tcix: Putative tre 75.8 1.7 3.6E-05 31.4 1.4 30 212-245 5-37 (44)
89 PRK14559 putative protein seri 75.4 1.8 3.9E-05 49.3 2.3 25 219-254 28-52 (645)
90 KOG3800 Predicted E3 ubiquitin 74.2 3.9 8.4E-05 41.5 4.0 48 60-116 2-52 (300)
91 PF00643 zf-B_box: B-box zinc 74.1 2.3 4.9E-05 30.0 1.8 27 219-252 4-32 (42)
92 PF13248 zf-ribbon_3: zinc-rib 73.7 1.8 3.9E-05 27.6 1.1 11 219-229 3-13 (26)
93 PF13240 zinc_ribbon_2: zinc-r 73.5 1.8 3.9E-05 26.9 1.0 10 220-229 1-10 (23)
94 KOG1952 Transcription factor N 73.4 2.4 5.2E-05 48.6 2.7 51 56-107 189-241 (950)
95 PRK00432 30S ribosomal protein 73.2 2.2 4.7E-05 31.9 1.6 28 216-245 18-47 (50)
96 COG5175 MOT2 Transcriptional r 73.0 1.6 3.6E-05 44.8 1.1 54 58-120 14-69 (480)
97 COG4647 AcxC Acetone carboxyla 72.8 8.6 0.00019 34.3 5.4 61 168-229 67-131 (165)
98 KOG1701 Focal adhesion adaptor 72.5 2.4 5.1E-05 45.1 2.2 11 60-70 276-286 (468)
99 KOG0317 Predicted E3 ubiquitin 70.9 0.64 1.4E-05 46.9 -2.3 35 214-254 235-270 (293)
100 COG5222 Uncharacterized conser 70.1 2.5 5.5E-05 42.7 1.7 43 59-112 275-318 (427)
101 PF09297 zf-NADH-PPase: NADH p 70.1 5.9 0.00013 26.4 3.0 28 217-244 2-30 (32)
102 PF10367 Vps39_2: Vacuolar sor 69.9 1.5 3.3E-05 37.4 0.1 32 57-88 77-108 (109)
103 KOG4445 Uncharacterized conser 69.8 2.3 5E-05 43.1 1.4 37 58-94 115-152 (368)
104 cd07630 BAR_SNX_like The Bin/A 69.5 95 0.002 30.1 12.4 63 372-434 131-193 (198)
105 PRK00398 rpoP DNA-directed RNA 69.4 4.3 9.4E-05 29.5 2.4 29 219-247 4-33 (46)
106 PHA03096 p28-like protein; Pro 68.9 2.7 5.9E-05 43.0 1.7 37 59-95 179-221 (284)
107 PF15227 zf-C3HC4_4: zinc fing 68.6 2.3 5E-05 30.4 0.8 28 221-253 1-28 (42)
108 KOG3002 Zn finger protein [Gen 68.2 7.7 0.00017 40.0 4.8 53 55-123 45-97 (299)
109 cd07621 BAR_SNX5_6 The Bin/Amp 67.4 1.1E+02 0.0024 30.2 12.4 60 378-437 156-215 (219)
110 KOG1493 Anaphase-promoting com 67.4 1.6 3.4E-05 35.4 -0.3 48 60-114 22-80 (84)
111 KOG2807 RNA polymerase II tran 65.7 2.4 5.2E-05 43.5 0.6 85 79-190 275-365 (378)
112 PLN03086 PRLI-interacting fact 65.6 11 0.00024 42.2 5.6 57 101-180 406-463 (567)
113 KOG3970 Predicted E3 ubiquitin 62.5 5.9 0.00013 38.6 2.5 55 58-114 50-104 (299)
114 cd07662 BAR_SNX6 The Bin/Amphi 61.2 1.3E+02 0.0028 29.6 11.5 60 378-437 155-214 (218)
115 PF14835 zf-RING_6: zf-RING of 61.0 3.9 8.5E-05 32.2 0.8 21 219-239 8-31 (65)
116 KOG2034 Vacuolar sorting prote 60.4 4.4 9.5E-05 46.9 1.5 37 57-93 816-852 (911)
117 PF13717 zinc_ribbon_4: zinc-r 60.0 8.8 0.00019 26.5 2.4 28 150-180 3-35 (36)
118 PF13719 zinc_ribbon_5: zinc-r 59.6 9.1 0.0002 26.6 2.4 28 150-180 3-35 (37)
119 PF02150 RNA_POL_M_15KD: RNA p 59.4 6.5 0.00014 27.0 1.6 27 150-179 2-29 (35)
120 PF08274 PhnA_Zn_Ribbon: PhnA 58.3 8.8 0.00019 25.6 2.0 25 220-245 4-29 (30)
121 KOG3579 Predicted E3 ubiquitin 57.8 9.7 0.00021 38.5 3.2 54 56-112 266-322 (352)
122 KOG2906 RNA polymerase III sub 57.3 7.8 0.00017 33.0 2.1 28 220-247 3-33 (105)
123 cd00021 BBOX B-Box-type zinc f 57.1 8.9 0.00019 26.2 2.1 26 220-252 2-29 (39)
124 KOG1941 Acetylcholine receptor 57.1 4.5 9.7E-05 42.6 0.7 49 56-112 363-413 (518)
125 PF14447 Prok-RING_4: Prokaryo 56.9 4 8.6E-05 31.1 0.3 45 58-116 7-51 (55)
126 COG5219 Uncharacterized conser 56.2 6.9 0.00015 45.6 2.1 52 56-115 1467-1523(1525)
127 KOG0320 Predicted E3 ubiquitin 56.1 2.7 5.9E-05 39.6 -0.9 30 174-229 149-178 (187)
128 PRK08665 ribonucleotide-diphos 55.8 6.4 0.00014 45.8 1.8 26 219-246 725-751 (752)
129 cd00194 UBA Ubiquitin Associat 54.5 21 0.00046 24.3 3.6 27 4-30 11-37 (38)
130 PF07191 zinc-ribbons_6: zinc- 54.2 11 0.00025 30.1 2.4 32 220-253 3-40 (70)
131 COG1198 PriA Primosomal protei 53.7 10 0.00022 43.9 2.9 35 218-252 444-484 (730)
132 TIGR00622 ssl1 transcription f 53.2 12 0.00025 32.9 2.6 38 150-190 56-101 (112)
133 COG1645 Uncharacterized Zn-fin 53.1 9.9 0.00022 34.2 2.2 24 218-250 28-51 (131)
134 KOG1940 Zn-finger protein [Gen 53.0 12 0.00025 38.2 2.9 47 56-112 156-204 (276)
135 PRK04023 DNA polymerase II lar 52.8 10 0.00022 44.8 2.7 33 145-187 622-660 (1121)
136 KOG2177 Predicted E3 ubiquitin 52.3 14 0.00029 36.6 3.4 24 220-250 88-112 (386)
137 KOG4275 Predicted E3 ubiquitin 52.2 6.2 0.00013 40.0 0.8 29 58-88 300-329 (350)
138 PRK14559 putative protein seri 51.7 10 0.00022 43.2 2.6 13 217-229 40-52 (645)
139 COG1998 RPS31 Ribosomal protei 51.5 11 0.00023 28.1 1.7 26 218-243 19-45 (51)
140 PRK05654 acetyl-CoA carboxylas 51.0 3.9 8.4E-05 42.1 -0.8 28 218-245 27-56 (292)
141 PF07282 OrfB_Zn_ribbon: Putat 50.9 13 0.00029 29.1 2.4 28 217-244 27-55 (69)
142 KOG1571 Predicted E3 ubiquitin 50.8 8 0.00017 40.4 1.4 44 56-114 303-346 (355)
143 TIGR02098 MJ0042_CXXC MJ0042 f 50.7 17 0.00037 25.0 2.7 27 151-180 4-35 (38)
144 KOG3039 Uncharacterized conser 50.3 11 0.00023 37.5 2.1 37 59-97 44-80 (303)
145 PLN03208 E3 ubiquitin-protein 49.9 5.2 0.00011 38.5 -0.1 31 218-253 18-48 (193)
146 PF00627 UBA: UBA/TS-N domain; 49.8 18 0.00038 24.9 2.6 24 5-28 13-36 (37)
147 cd07663 BAR_SNX5 The Bin/Amphi 49.6 2.7E+02 0.0058 27.5 12.7 60 378-437 155-214 (218)
148 KOG3268 Predicted E3 ubiquitin 49.5 16 0.00036 34.4 3.1 57 57-115 164-228 (234)
149 PF09538 FYDLN_acid: Protein o 49.5 9.3 0.0002 33.4 1.4 25 219-245 10-36 (108)
150 KOG0978 E3 ubiquitin ligase in 49.4 4.8 0.0001 45.8 -0.5 30 175-229 660-689 (698)
151 smart00165 UBA Ubiquitin assoc 48.3 25 0.00054 23.9 3.2 26 4-29 11-36 (37)
152 PF06677 Auto_anti-p27: Sjogre 48.1 15 0.00032 26.3 2.0 22 219-242 18-41 (41)
153 cd07622 BAR_SNX4 The Bin/Amphi 47.8 2.7E+02 0.0058 26.9 14.2 96 325-434 99-194 (201)
154 TIGR00595 priA primosomal prot 47.7 16 0.00035 40.5 3.3 34 219-252 223-262 (505)
155 cd07666 BAR_SNX7 The Bin/Amphi 47.5 3.1E+02 0.0067 27.5 12.8 99 325-434 140-238 (243)
156 KOG4460 Nuclear pore complex, 47.0 4.6E+02 0.01 29.4 14.6 38 378-416 628-665 (741)
157 PF12906 RINGv: RING-variant d 45.5 16 0.00034 26.8 1.9 33 61-93 1-38 (47)
158 PF14446 Prok-RING_1: Prokaryo 45.0 18 0.00039 27.5 2.1 32 58-89 5-38 (54)
159 PF02318 FYVE_2: FYVE-type zin 44.5 37 0.0008 29.9 4.5 42 217-259 53-95 (118)
160 PRK14714 DNA polymerase II lar 44.1 17 0.00036 44.1 2.7 16 380-395 797-812 (1337)
161 PF05290 Baculo_IE-1: Baculovi 44.1 18 0.00038 32.7 2.3 53 55-114 77-131 (140)
162 CHL00174 accD acetyl-CoA carbo 43.8 5.4 0.00012 41.0 -1.1 28 218-245 38-67 (296)
163 PF14445 Prok-RING_2: Prokaryo 43.8 5.1 0.00011 29.8 -0.9 34 57-90 6-40 (57)
164 PF14369 zf-RING_3: zinc-finge 43.4 20 0.00043 24.7 2.0 28 150-180 3-31 (35)
165 PF14803 Nudix_N_2: Nudix N-te 43.4 21 0.00046 24.4 2.1 25 219-243 1-30 (34)
166 PF10267 Tmemb_cc2: Predicted 43.2 2.1E+02 0.0045 30.8 10.6 26 372-397 47-72 (395)
167 PRK14714 DNA polymerase II lar 43.2 16 0.00034 44.3 2.4 10 219-228 668-677 (1337)
168 KOG2932 E3 ubiquitin ligase in 43.2 8.3 0.00018 39.4 0.1 53 146-234 87-139 (389)
169 KOG3053 Uncharacterized conser 43.1 19 0.00042 36.0 2.6 55 57-113 19-80 (293)
170 TIGR01384 TFS_arch transcripti 43.0 16 0.00034 31.3 1.8 23 220-244 2-25 (104)
171 PF12773 DZR: Double zinc ribb 43.0 10 0.00022 27.8 0.5 11 219-229 30-40 (50)
172 PF13834 DUF4193: Domain of un 42.8 9.9 0.00021 32.5 0.5 32 55-86 67-98 (99)
173 PRK14873 primosome assembly pr 42.4 20 0.00042 41.3 3.0 34 219-252 393-431 (665)
174 KOG4362 Transcriptional regula 42.1 7.7 0.00017 44.0 -0.3 53 57-118 20-72 (684)
175 COG1997 RPL43A Ribosomal prote 41.8 22 0.00049 29.6 2.4 28 218-245 35-63 (89)
176 TIGR00515 accD acetyl-CoA carb 41.6 6.4 0.00014 40.3 -1.0 28 218-245 26-55 (285)
177 KOG2114 Vacuolar assembly/sort 41.3 17 0.00037 42.1 2.2 40 59-112 841-880 (933)
178 KOG4759 Ribosome recycling fac 41.2 1.9E+02 0.0042 29.2 9.3 66 374-439 197-262 (263)
179 TIGR03655 anti_R_Lar restricti 40.6 23 0.00051 26.5 2.2 11 219-229 2-12 (53)
180 PF08746 zf-RING-like: RING-li 40.2 26 0.00056 25.2 2.3 41 61-107 1-42 (43)
181 PHA02929 N1R/p28-like protein; 39.6 8.2 0.00018 38.5 -0.5 32 172-229 196-227 (238)
182 PRK05580 primosome assembly pr 39.3 25 0.00054 40.6 3.2 34 219-252 391-430 (679)
183 KOG3161 Predicted E3 ubiquitin 39.1 13 0.00027 41.8 0.7 36 58-93 11-48 (861)
184 smart00336 BBOX B-Box-type zin 37.4 32 0.00069 23.7 2.4 27 219-252 4-32 (42)
185 PF06906 DUF1272: Protein of u 37.3 13 0.00029 28.3 0.4 45 59-115 6-52 (57)
186 PHA02926 zinc finger-like prot 36.4 7.6 0.00017 38.1 -1.3 35 175-229 196-230 (242)
187 PF03119 DNA_ligase_ZBD: NAD-d 36.0 34 0.00074 22.3 2.1 20 220-239 1-20 (28)
188 PF01363 FYVE: FYVE zinc finge 35.8 16 0.00034 28.7 0.6 37 56-92 7-45 (69)
189 PF08580 KAR9: Yeast cortical 35.8 3.8E+02 0.0082 31.1 11.9 22 376-397 272-293 (683)
190 PF01599 Ribosomal_S27: Riboso 35.6 31 0.00067 25.5 2.1 26 218-243 18-46 (47)
191 COG5432 RAD18 RING-finger-cont 35.1 15 0.00033 37.2 0.6 32 219-257 26-59 (391)
192 PF02891 zf-MIZ: MIZ/SP-RING z 34.7 29 0.00063 25.8 1.9 46 59-112 3-49 (50)
193 PF02845 CUE: CUE domain; Int 34.7 73 0.0016 22.4 3.9 27 5-31 14-40 (42)
194 KOG2856 Adaptor protein PACSIN 34.4 6E+02 0.013 27.1 12.2 81 372-469 216-299 (472)
195 KOG0994 Extracellular matrix g 34.3 9.8E+02 0.021 29.6 14.6 74 368-442 1224-1303(1758)
196 PF07975 C1_4: TFIIH C1-like d 34.2 17 0.00037 27.3 0.5 22 170-191 20-42 (51)
197 PF14569 zf-UDP: Zinc-binding 34.1 46 0.001 27.2 3.0 49 57-114 8-61 (80)
198 COG5574 PEX10 RING-finger-cont 34.1 11 0.00023 37.9 -0.7 37 56-92 93-132 (271)
199 COG0777 AccD Acetyl-CoA carbox 34.1 14 0.00029 37.5 0.0 29 217-245 27-57 (294)
200 cd07624 BAR_SNX7_30 The Bin/Am 34.0 4.3E+02 0.0093 25.3 12.2 53 382-434 143-195 (200)
201 COG2888 Predicted Zn-ribbon RN 34.0 28 0.00061 26.9 1.7 6 220-225 29-34 (61)
202 COG5194 APC11 Component of SCF 33.9 36 0.00078 28.0 2.4 36 58-93 31-69 (88)
203 KOG0309 Conserved WD40 repeat- 33.5 32 0.0007 39.4 2.8 49 57-114 1027-1075(1081)
204 PRK14892 putative transcriptio 33.5 31 0.00067 29.7 2.1 27 218-244 21-51 (99)
205 PRK12495 hypothetical protein; 32.4 46 0.00099 32.7 3.3 27 217-252 41-67 (226)
206 PF06827 zf-FPG_IleRS: Zinc fi 32.2 33 0.00072 22.3 1.7 24 219-242 2-28 (30)
207 PF14569 zf-UDP: Zinc-binding 31.9 23 0.00049 29.0 0.9 54 157-235 14-68 (80)
208 PRK11827 hypothetical protein; 30.9 44 0.00095 26.0 2.4 25 219-243 9-34 (60)
209 PRK13182 racA polar chromosome 30.9 3.4E+02 0.0074 25.7 8.9 60 374-434 86-145 (175)
210 COG5236 Uncharacterized conser 30.7 31 0.00068 35.9 2.0 48 56-113 59-106 (493)
211 COG2178 Predicted RNA-binding 30.7 5.1E+02 0.011 25.2 11.8 52 295-346 38-92 (204)
212 PF08792 A2L_zn_ribbon: A2L zi 29.5 60 0.0013 22.0 2.6 12 218-229 3-14 (33)
213 PF14471 DUF4428: Domain of un 29.3 41 0.00089 25.2 1.9 30 60-90 1-30 (51)
214 TIGR00686 phnA alkylphosphonat 29.2 40 0.00086 29.3 2.0 26 219-245 3-29 (109)
215 smart00659 RPOLCX RNA polymera 28.6 48 0.001 24.0 2.1 9 220-228 21-29 (44)
216 PF14149 YhfH: YhfH-like prote 28.3 4.4 9.6E-05 28.3 -3.1 26 216-241 11-37 (37)
217 PRK14811 formamidopyrimidine-D 28.3 39 0.00085 34.2 2.2 22 218-239 235-258 (269)
218 KOG2164 Predicted E3 ubiquitin 28.2 21 0.00047 39.0 0.3 28 218-252 186-215 (513)
219 PF05605 zf-Di19: Drought indu 27.8 91 0.002 23.2 3.7 45 58-119 2-46 (54)
220 PRK09710 lar restriction allev 27.8 54 0.0012 25.8 2.4 14 217-230 5-18 (64)
221 COG5109 Uncharacterized conser 27.3 53 0.0011 33.9 2.9 50 57-113 335-385 (396)
222 COG0266 Nei Formamidopyrimidin 27.3 42 0.00091 34.2 2.2 25 218-242 245-272 (273)
223 smart00546 CUE Domain that may 27.3 1E+02 0.0022 21.7 3.7 27 5-31 15-41 (43)
224 PF05633 DUF793: Protein of un 27.2 3.4E+02 0.0074 29.1 9.0 18 415-432 364-381 (389)
225 PF15616 TerY-C: TerY-C metal 27.2 52 0.0011 29.7 2.5 21 156-183 81-101 (131)
226 PF07800 DUF1644: Protein of u 27.2 66 0.0014 30.0 3.2 36 58-95 2-50 (162)
227 TIGR00577 fpg formamidopyrimid 27.1 43 0.00094 34.0 2.3 22 218-239 245-268 (272)
228 PRK01103 formamidopyrimidine/5 27.0 44 0.00094 34.0 2.3 25 218-242 245-272 (274)
229 PF06844 DUF1244: Protein of u 26.8 43 0.00092 26.5 1.6 17 81-97 11-27 (68)
230 PRK14810 formamidopyrimidine-D 26.8 43 0.00094 34.0 2.2 25 218-242 244-271 (272)
231 TIGR02300 FYDLN_acid conserved 26.4 37 0.0008 30.4 1.4 25 219-244 10-35 (129)
232 PRK13945 formamidopyrimidine-D 26.3 45 0.00097 34.0 2.3 25 218-242 254-281 (282)
233 PF15358 TSKS: Testis-specific 26.0 4.7E+02 0.01 28.2 9.5 88 281-397 123-212 (558)
234 PF08926 DUF1908: Domain of un 26.0 4.1E+02 0.009 27.1 8.8 21 375-395 186-206 (282)
235 PRK10445 endonuclease VIII; Pr 25.3 50 0.0011 33.4 2.3 25 218-242 235-262 (263)
236 KOG2930 SCF ubiquitin ligase, 25.1 57 0.0012 28.2 2.2 23 77-107 80-102 (114)
237 COG3813 Uncharacterized protei 25.0 26 0.00057 28.1 0.2 44 59-114 6-51 (84)
238 PF07503 zf-HYPF: HypF finger; 24.5 51 0.0011 22.7 1.5 31 82-114 1-31 (35)
239 PF12861 zf-Apc11: Anaphase-pr 24.5 26 0.00056 29.2 0.1 35 219-256 33-67 (85)
240 PF08317 Spc7: Spc7 kinetochor 24.4 8.1E+02 0.017 25.4 12.9 10 193-202 76-85 (325)
241 TIGR00373 conserved hypothetic 24.2 96 0.0021 28.8 3.8 32 145-179 105-137 (158)
242 COG1594 RPB9 DNA-directed RNA 24.1 59 0.0013 28.5 2.3 27 219-245 3-32 (113)
243 KOG2150 CCR4-NOT transcription 24.0 1.1E+03 0.023 26.7 13.2 25 370-394 119-143 (575)
244 PF03833 PolC_DP2: DNA polymer 23.8 26 0.00057 40.8 0.0 57 377-433 776-836 (900)
245 KOG0825 PHD Zn-finger protein 23.4 48 0.001 38.2 1.9 49 58-116 123-172 (1134)
246 PHA02825 LAP/PHD finger-like p 23.4 72 0.0016 29.8 2.8 49 57-114 7-58 (162)
247 PRK04778 septation ring format 23.4 1.1E+03 0.024 26.6 12.8 78 343-441 154-232 (569)
248 KOG0801 Predicted E3 ubiquitin 23.3 29 0.00063 32.3 0.2 29 55-83 174-203 (205)
249 smart00064 FYVE Protein presen 22.3 61 0.0013 25.2 1.8 36 58-93 10-47 (68)
250 smart00531 TFIIE Transcription 22.3 1.2E+02 0.0027 27.6 4.1 18 146-166 96-113 (147)
251 COG1623 Predicted nucleic-acid 22.0 2.7E+02 0.0057 28.8 6.6 31 276-306 151-181 (349)
252 PRK09521 exosome complex RNA-b 22.0 64 0.0014 30.8 2.3 25 220-245 151-176 (189)
253 COG3416 Uncharacterized protei 21.9 6.3E+02 0.014 24.8 8.8 30 444-473 92-122 (233)
254 KOG2906 RNA polymerase III sub 21.9 97 0.0021 26.5 3.0 27 150-179 2-30 (105)
255 cd00065 FYVE FYVE domain; Zinc 21.8 52 0.0011 24.5 1.3 35 59-93 3-39 (57)
256 PRK12286 rpmF 50S ribosomal pr 21.7 57 0.0012 25.1 1.5 13 217-229 26-38 (57)
257 PRK10220 hypothetical protein; 21.7 67 0.0015 28.0 2.1 15 219-233 4-18 (111)
258 PF13453 zf-TFIIB: Transcripti 21.7 67 0.0014 22.6 1.7 29 220-253 1-29 (41)
259 KOG2629 Peroxisomal membrane a 21.6 9E+02 0.019 24.9 10.9 14 346-359 103-116 (300)
260 TIGR01206 lysW lysine biosynth 21.6 98 0.0021 23.6 2.7 27 151-180 4-32 (54)
261 PRK04023 DNA polymerase II lar 21.6 48 0.001 39.4 1.5 31 216-252 624-660 (1121)
262 PF05278 PEARLI-4: Arabidopsis 21.3 8.8E+02 0.019 24.7 12.1 53 328-395 167-219 (269)
263 COG2051 RPS27A Ribosomal prote 21.2 1.1E+02 0.0024 24.3 3.0 31 150-183 20-51 (67)
264 PF10241 KxDL: Uncharacterized 21.2 3.6E+02 0.0079 22.4 6.4 34 286-319 43-76 (88)
265 PRK06266 transcription initiat 21.0 1.1E+02 0.0024 29.0 3.7 32 145-179 113-145 (178)
266 PF14353 CpXC: CpXC protein 21.0 41 0.00088 29.8 0.7 50 103-165 2-51 (128)
267 PF01428 zf-AN1: AN1-like Zinc 20.9 56 0.0012 23.3 1.2 16 171-186 13-29 (43)
268 PF03854 zf-P11: P-11 zinc fin 20.8 41 0.00089 24.9 0.5 44 59-116 3-47 (50)
269 PF00098 zf-CCHC: Zinc knuckle 20.6 60 0.0013 18.8 1.1 16 180-195 2-17 (18)
270 PF15616 TerY-C: TerY-C metal 20.2 72 0.0016 28.9 2.0 35 217-251 76-113 (131)
271 PF10122 Mu-like_Com: Mu-like 20.2 44 0.00096 25.1 0.6 24 220-243 6-32 (51)
272 KOG2979 Protein involved in DN 20.2 71 0.0015 32.1 2.2 48 58-112 176-223 (262)
273 PLN02189 cellulose synthase 20.1 64 0.0014 38.7 2.1 59 151-237 36-95 (1040)
274 TIGR01031 rpmF_bact ribosomal 20.1 62 0.0013 24.6 1.4 13 217-229 25-37 (55)
275 KOG2932 E3 ubiquitin ligase in 20.1 44 0.00096 34.4 0.8 28 218-252 90-120 (389)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.5e-65 Score=544.56 Aligned_cols=410 Identities=40% Similarity=0.778 Sum_probs=363.0
Q ss_pred CccccCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCCCCCCCcccccccccccccccccCceecCCCC
Q 009562 1 MELLSLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPMLPLSSTVMCDICMEEVAGDKATKMDCGH 80 (532)
Q Consensus 1 ~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l~CgH 80 (532)
|++|++++.+|++||.||.|+++++++.|++ ..+.++..+|+.+.. ......+|.||++.++. .+..+.|||
T Consensus 20 ~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~------~~~~~~~c~ic~~~~~~-~~~~~~c~H 91 (444)
T KOG1815|consen 20 SDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWP------KKKGDVQCGICVESYDG-EIIGLGCGH 91 (444)
T ss_pred HHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccC------CCCccccCCcccCCCcc-hhhhcCCCc
Confidence 6899999999999999999999999999996 566788888865543 23456899999999775 677889999
Q ss_pred cccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhcCCCh-hHHHHHHHHHHHHhhhcccccccCCCCCCCC
Q 009562 81 CFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHP-NLAEKFERFLLESFIEDNKMVKWCPSTPHCG 159 (532)
Q Consensus 81 ~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~-e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~ 159 (532)
.||..||..|+..+|.+|....|+||..+|.+.+..+.|..+++ + +..++|.++++.+||+.+..++|||+ |+|+
T Consensus 92 ~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s---~~~~~~ky~~~i~~syve~~~~lkwCP~-~~C~ 167 (444)
T KOG1815|consen 92 PFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVS---DKEDKEKYQRYILRSYVEDNVPLKWCPA-PGCG 167 (444)
T ss_pred HHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecC---CHHHHHHHHHHHHHHHHhcCCccccCCC-CCCC
Confidence 99999999999999998875559999999999999999999998 4 58999999999999999999999995 9999
Q ss_pred ceEEeccccceeeeecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCcceeecCCCCeeEe
Q 009562 160 NAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC 239 (532)
Q Consensus 160 ~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC 239 (532)
+++.........|.|.|++.|||.|+.+||.|.+|..+..|+++..+++++.+||..|+++||+|.++|||++|||||+|
T Consensus 168 ~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~ 247 (444)
T KOG1815|consen 168 LAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTC 247 (444)
T ss_pred ceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCcccccc
Confidence 99997555566799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred c---cCceeecccccccCCCCCccccCCccccCccchHHHH-HHHHHHHhhhhhHHHHHHhhhhhhHHHHHHHHHHHHHH
Q 009562 240 I---CGQAFCWLCGGATGRDHTWSRIAGHSCGRYKEDKAKK-TERAKRELYRYMHYHNRYKAHTDSFKLESKLKETVLEK 315 (532)
Q Consensus 240 ~---C~~~FCw~C~~~~~~~H~w~~h~g~~C~~~~~~~~~~-~~~~~~~l~ry~~y~~R~~~h~~s~k~e~~l~~~i~~k 315 (532)
. |++.|||+|++.|.. |+.+. ++.|++|..+.... ...++..+.||.|||.||++|..+++++..+...+++.
T Consensus 248 ~~~~c~~~FCw~Cl~~~~~-h~~~~--~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~~~q~s~~~~~~~~~~~~~~ 324 (444)
T KOG1815|consen 248 KSASCKHEFCWVCLASLSD-HGSST--GYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWMEHQVSLKLEGKLLSKVEEV 324 (444)
T ss_pred ccCCcCCeeceeeeccccc-ccccc--eeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHHhhhhhhhhhhhhHHHHHHH
Confidence 4 999999999988754 33322 79999999877655 77888999999999999999999999998777666544
Q ss_pred -HHHHhhh-hccccchhHHHHHHHHHHHHHHhhhccccceeeccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 316 -VSISEER-ESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLS 393 (532)
Q Consensus 316 -~~~~~~~-~~~~~~~~~l~~a~~~l~~~R~vL~~Sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~ 393 (532)
...+... ...+.+++|+.+++.+|+++|++|+|||+|+||+..+ .+.++||++|.+||..+|.|+
T Consensus 325 ~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~~-------------~~~~~fe~~q~~~~~~~e~ls 391 (444)
T KOG1815|consen 325 KKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSEN-------------NKRNLFEDNQTDLESAVEPLS 391 (444)
T ss_pred hhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhccc-------------chhhhhHHHHHHHhhhhhhhH
Confidence 3333322 2347799999999999999999999999999999732 244899999999999999999
Q ss_pred HHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 009562 394 KFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLL 438 (532)
Q Consensus 394 ~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~ 438 (532)
..++.++...+.+++..+|+++.+++.++++++++++..++++|-
T Consensus 392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 436 (444)
T KOG1815|consen 392 SCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLE 436 (444)
T ss_pred HHhccccccCCcccHHHHHhhccccchhhhhHHHHHHHHHHhccc
Confidence 999998888888999999999999999999999999999998875
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-34 Score=301.35 Aligned_cols=267 Identities=30% Similarity=0.605 Sum_probs=205.3
Q ss_pred HHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCCC-----------CC--CC-cccccccccccccc-cccCce
Q 009562 10 HARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDAD-----------PM--LP-LSSTVMCDICMEEV-AGDKAT 74 (532)
Q Consensus 10 ~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~-----------~~--~~-~~~~~~C~IC~e~~-~~~~~~ 74 (532)
.+......+.|++..|.+.+.. ....+.....+.+..+.. .. .+ .....+|.||+.+. ..+.++
T Consensus 85 v~~~~~~~~~~~~~~l~~~v~~-~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s~~~~~~~~~~C~iC~~e~~~~~~~f 163 (384)
T KOG1812|consen 85 VAGREKPEQHRKIVLLVELVQR-IREQLTSSEPILVPKNADIKFAYKLAREAIVSQLPSKLPKEECGICFVEDPEAEDMF 163 (384)
T ss_pred HhhhhhHHHHHHHHHHHHHHHH-HHHHhhcccceecccchhhHHHHHHHHHhhccccccccccccCccCccccccHhhhH
Confidence 4555566677777777777753 344444444443322210 00 11 12367899999553 333555
Q ss_pred e-cCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhcCCChhHHHHHHHHHHHHhhhcccccccCC
Q 009562 75 K-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCP 153 (532)
Q Consensus 75 ~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP 153 (532)
. ..|+|.||.+||++|+..+...| ..++||..+|+..++.+....+|+ +++.+.|++.+.+.++.....+ +||
T Consensus 164 ~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt---~kl~e~~e~~~~e~~i~~~~~~-ycp 237 (384)
T KOG1812|consen 164 SVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLT---PKLREMWEQRLKEEVIPSLDRV-YCP 237 (384)
T ss_pred HHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcC---HHHHHHHHHHHHHHhhhhhhcc-cCC
Confidence 4 48999999999999999984444 579999999999999999999999 8899999999999999988888 999
Q ss_pred CCCCCCceEEecc----ccceeeeec-CCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCcce
Q 009562 154 STPHCGNAIRVEE----VEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPV 228 (532)
Q Consensus 154 ~~p~C~~~i~~~~----~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~I 228 (532)
.|+|...+.... .......|+ |+..||..|+.+||.+.+|.++++|......+..+++++..+|++||+|+..|
T Consensus 238 -~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~i 316 (384)
T KOG1812|consen 238 -YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMI 316 (384)
T ss_pred -CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceee
Confidence 699998877433 223334674 99999999999999999999999999887888889999999999999999999
Q ss_pred eecCCCCeeEeccCceeecccccccCCCCCccccCC--ccccCccchHHHHHHHHHHHhhhhhHHHHHHhhhhhhHHHH
Q 009562 229 EKNGGCNLVSCICGQAFCWLCGGATGRDHTWSRIAG--HSCGRYKEDKAKKTERAKRELYRYMHYHNRYKAHTDSFKLE 305 (532)
Q Consensus 229 EKn~GCnhMtC~C~~~FCw~C~~~~~~~H~w~~h~g--~~C~~~~~~~~~~~~~~~~~l~ry~~y~~R~~~h~~s~k~e 305 (532)
|+++|||||+|+||++|||.|+++|. .+++ +.|.++... ++|+.++.+|.....++
T Consensus 317 e~~~GCnhm~CrC~~~fcy~C~~~~~------~~~~~~~~~~r~~~~---------------~~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 317 ELSEGCNHMTCRCGHQFCYMCGGDWK------THNGECYECCRYKES---------------THYFEDDENHDKSIQLE 374 (384)
T ss_pred eecCCcceEEeeccccchhhcCcchh------hCCccccCccccccc---------------ccccccccccccccccc
Confidence 99999999999999999999999963 2222 455555543 67777777776665443
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-33 Score=286.14 Aligned_cols=205 Identities=27% Similarity=0.666 Sum_probs=174.9
Q ss_pred ccccccccccccccc-cCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhcCCChhHHHHH
Q 009562 56 SSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKF 134 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 134 (532)
...+.|.|||++... ..+..++|+|.||+.|++.|++..|++|.+..++||.++|+...++..++.+|. .++++||
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg---~EL~arY 258 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVG---DELFARY 258 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHH---HHHHHHH
Confidence 356899999999766 456667999999999999999999999999999999999999999999999999 8999999
Q ss_pred HHHHHHHhhhcccccccCCCCCCCCceEEeccccceeeeec-CCCeeecCcccCCCCCCChhhh--------HHHHh---
Q 009562 135 ERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMW--------DLWAK--- 202 (532)
Q Consensus 135 ~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~--------~~w~~--- 202 (532)
+.+++++.++...++++|| .+.|..++. .+.....+.|. |..+||+.|+..||...+|... ..|..
T Consensus 259 e~l~lqk~l~~msdv~yCP-r~~Cq~p~~-~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCP-RACCQLPVK-QDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE 336 (445)
T ss_pred HHHHHHHHHHhhcccccCC-hhhccCccc-cCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence 9999999999999999999 589999884 44444568995 9999999999999999899643 12211
Q ss_pred ----------------hhhchHHHHHHHHcCccCCCCCCcceeecCCCCeeEe-ccCceeecccccccCCCCCccccCCc
Q 009562 203 ----------------KCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATGRDHTWSRIAGH 265 (532)
Q Consensus 203 ----------------~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~~~H~w~~h~g~ 265 (532)
...++-.+.+|+..|.|+||+|+++|||++|||+|+| .|++.|||+|.....+..+|.++.+-
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 1113345668999999999999999999999999999 59999999999987766667665543
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=1.9e-24 Score=211.74 Aligned_cols=197 Identities=29% Similarity=0.634 Sum_probs=148.1
Q ss_pred cccccccccccccccccCceecCCC--CcccHHHHHHHHHhhhccCCc-------ccccccccccccccC-hHHHHHHhc
Q 009562 55 LSSTVMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQS-------KRIRCMAHKCNAICD-EAVVRNLVS 124 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~i~~g~~-------~~i~CP~~~C~~~~~-~~~i~~ll~ 124 (532)
+....+|..|-+.-+ .+..++|. |..|.+|++.|..+.+++.+. ..+.||. +|...+- +-.--++|.
T Consensus 218 N~~ni~C~~Ctdv~~--~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg 294 (446)
T KOG0006|consen 218 NSRNITCITCTDVRS--PVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCcc--ceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 566789999988733 55667898 999999999999999987663 2356664 4655432 222234677
Q ss_pred CCChhHHHHHHHHHHHHhhhcccccccCCCCCCCCceEEeccccceeeeec--CCCeeecCcccCCCCCC----------
Q 009562 125 KKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA--CGAQFCFSCLSEAHSPC---------- 192 (532)
Q Consensus 125 ~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--C~~~fC~~C~~~~H~p~---------- 192 (532)
.+.|.+|+++..+.+|.....+ .|| .|+||..+..+++. ..|+|. ||..||..|++.+|.+-
T Consensus 295 ---~e~Y~rYQr~atEe~vlq~gGV-lCP-~pgCG~gll~EPD~-rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t 368 (446)
T KOG0006|consen 295 ---EEQYNRYQRYATEECVLQMGGV-LCP-RPGCGAGLLPEPDQ-RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGT 368 (446)
T ss_pred ---hhHHHHHHHhhhhhheeecCCE-ecC-CCCCCcccccCCCC-CcccCCCCchhHhHHHHHhhhccccceeeeccccc
Confidence 7899999999999999888765 899 79999998877754 458994 99999999999999852
Q ss_pred -Chhhh-H-HHHhhhhchHHHHHHHHcCccCCCCCCcceeecCCCCeeEe-c--cCceeecccccccCCCCCcc
Q 009562 193 -SCSMW-D-LWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCNLVSC-I--CGQAFCWLCGGATGRDHTWS 260 (532)
Q Consensus 193 -~C~~~-~-~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCnhMtC-~--C~~~FCw~C~~~~~~~H~w~ 260 (532)
+|... . +-.....-+..+..-|+..||+||+|+.|.||||||+||.| + ||.+|||.|+-.|.+.-.|.
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~Cmgd 442 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGD 442 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccc
Confidence 13210 0 00000111334444578899999999999999999999999 4 99999999999998765543
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.18 E-value=3.6e-11 Score=94.36 Aligned_cols=62 Identities=53% Similarity=1.092 Sum_probs=55.1
Q ss_pred HHHHHHHHHHhhhcccccccCCCCCCCCceEEec-cccceeeee-cCCCeeecCcccCCCCCCCh
Q 009562 132 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE-EVEVCEVEC-ACGAQFCFSCLSEAHSPCSC 194 (532)
Q Consensus 132 eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 194 (532)
++|++++++++|+.++.++||| +|+|+.++... +.....|.| .|+..||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP-~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCP-APDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCC-CCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4789999999999988999999 79999999986 345567999 59999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.06 E-value=3.5e-11 Score=94.33 Aligned_cols=62 Identities=35% Similarity=0.960 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhhhcccccccCCCCCCCCceEEeccccce-eeeec-CCCeeecCcccCCCCCCCh
Q 009562 132 EKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVC-EVECA-CGAQFCFSCLSEAHSPCSC 194 (532)
Q Consensus 132 eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-C~~~fC~~C~~~~H~p~~C 194 (532)
++|++++++.+++.++.++||| +|+|+.++...+.... .++|+ |++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp-~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCP-NPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--T-TSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCC-CCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 5788999999998888999999 6999999997775444 48997 9999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.64 E-value=1.4e-08 Score=73.12 Aligned_cols=41 Identities=24% Similarity=0.740 Sum_probs=30.5
Q ss_pred cccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 61 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 61 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
|+||++.+. ++++++|||+||..|+..++...-. ..+.||.
T Consensus 1 CpiC~~~~~--~Pv~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFK--DPVSLPCGHSFCRSCLERLWKEPSG----SGFSCPE 41 (42)
T ss_dssp ETTTTSB-S--SEEE-SSSSEEEHHHHHHHHCCSSS----ST---SS
T ss_pred CCccchhhC--CccccCCcCHHHHHHHHHHHHccCC----cCCCCcC
Confidence 899999977 9999999999999999999976322 2278886
No 8
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.23 E-value=6.7e-07 Score=63.30 Aligned_cols=37 Identities=30% Similarity=0.872 Sum_probs=29.5
Q ss_pred cccccccccccCc-eecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 61 CDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 61 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
|+||++.+. ++ +.++|||.||.+||.+|+... .+||.
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 899999866 56 577999999999999998762 57876
No 9
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.20 E-value=1.1e-06 Score=62.67 Aligned_cols=39 Identities=31% Similarity=0.867 Sum_probs=32.5
Q ss_pred cccccccccccCce-ecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 61 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 61 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
|+||++.+. ++. .++|||.||..||.+++.. . ..+.||.
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 899999866 555 7799999999999999997 2 3478986
No 10
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.18 E-value=9.1e-07 Score=64.28 Aligned_cols=40 Identities=38% Similarity=0.836 Sum_probs=33.0
Q ss_pred cccccccccc-ccCceecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 60 MCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 60 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
+|+||++++. .+.++.++|||.||.+|+..|+... .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 6999999985 4567778999999999999999762 38887
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.10 E-value=2.4e-06 Score=81.08 Aligned_cols=66 Identities=23% Similarity=0.512 Sum_probs=48.6
Q ss_pred cccccccccccccccccCceecCCCCcccHHHHHHHHHhhhcc--------CCcccccccccccccccChHHHHHHhc
Q 009562 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE--------GQSKRIRCMAHKCNAICDEAVVRNLVS 124 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~--------g~~~~i~CP~~~C~~~~~~~~i~~ll~ 124 (532)
....++|+||++.+. +++.++|||.||..|+..|+...-.. ......+||. |+..+....+..+..
T Consensus 15 ~~~~~~CpICld~~~--dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 15 SGGDFDCNICLDQVR--DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCCccCCccCCCcCC--CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 345789999999865 88889999999999999997642110 0113579999 999887765554443
No 12
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=2e-06 Score=79.69 Aligned_cols=55 Identities=24% Similarity=0.626 Sum_probs=43.8
Q ss_pred cccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH
Q 009562 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 119 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i 119 (532)
.+..+.|+||++.+....+++..|||.||..|++.-+.. ..+||. |...++..++
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhhh
Confidence 345689999999998777788999999999999987764 258999 6656655443
No 13
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.99 E-value=4e-06 Score=60.58 Aligned_cols=41 Identities=32% Similarity=0.783 Sum_probs=23.0
Q ss_pred cccccccccc--cCceecCCCCcccHHHHHHHHHhhhccCCccccccc
Q 009562 61 CDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCM 106 (532)
Q Consensus 61 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP 106 (532)
|+||.+ +.. ..++.|+|||.||.+|+.+.+.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 642 2367789999999999999988532 1358887
No 14
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.89 E-value=1.9e-05 Score=61.60 Aligned_cols=37 Identities=38% Similarity=0.908 Sum_probs=33.9
Q ss_pred CccCCC--CCCcceeecC--CCCeeEe-ccCceeeccccccc
Q 009562 217 HTKPCP--KCHKPVEKNG--GCNLVSC-ICGQAFCWLCGGAT 253 (532)
Q Consensus 217 ~tK~CP--kC~~~IEKn~--GCnhMtC-~C~~~FCw~C~~~~ 253 (532)
+.+.|| +|+..|+..+ |.++|+| .|++.|||.|+.+|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 568899 9999999965 9999999 79999999999996
No 15
>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=97.85 E-value=1.3e-05 Score=59.83 Aligned_cols=46 Identities=26% Similarity=0.709 Sum_probs=36.5
Q ss_pred ccccccccccccccCceecCCCCc-ccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
...|.||++... +++.++|||. ||..|+..++.. ..+||. |+..+.
T Consensus 2 ~~~C~iC~~~~~--~~~~~pCgH~~~C~~C~~~~~~~--------~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--DVVLLPCGHLCFCEECAERLLKR--------KKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--SEEEETTCEEEEEHHHHHHHHHT--------TSBBTT--TTBB-S
T ss_pred cCCCccCCccCC--ceEEeCCCChHHHHHHhHHhccc--------CCCCCc--CChhhc
Confidence 468999999854 6778899999 999999999882 368998 887653
No 16
>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=97.80 E-value=9e-06 Score=63.43 Aligned_cols=37 Identities=43% Similarity=1.110 Sum_probs=28.0
Q ss_pred CccCCCC--CCcceeecCCCCe--eEec-cCceeeccccccc
Q 009562 217 HTKPCPK--CHKPVEKNGGCNL--VSCI-CGQAFCWLCGGAT 253 (532)
Q Consensus 217 ~tK~CPk--C~~~IEKn~GCnh--MtC~-C~~~FCw~C~~~~ 253 (532)
+.+.||+ |...|++..|.++ |+|. |++.|||.|+++|
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 4579988 9999999999999 9996 9999999999996
No 17
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.79 E-value=2e-05 Score=56.20 Aligned_cols=43 Identities=33% Similarity=0.869 Sum_probs=33.1
Q ss_pred ccccccccccccCceec-CCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 60 MCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 60 ~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
+|+||++.+. +++.+ +|||.||..|+..|+.. + ..+||. |+..
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~----~---~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS----G---KNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh----C---cCCCCC--CCCc
Confidence 5999999873 44444 69999999999999875 2 367987 7653
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.76 E-value=1.7e-05 Score=57.60 Aligned_cols=42 Identities=31% Similarity=0.886 Sum_probs=33.3
Q ss_pred ccccccccccc-cCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccc
Q 009562 60 MCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 111 (532)
Q Consensus 60 ~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 111 (532)
.|+||++.+.. ..++.++|||.||..|+.... . ..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-----~---~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-----G---KSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-----C---CCCCCcC--CC
Confidence 49999999843 356667999999999999987 1 3589998 65
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=1.9e-05 Score=76.30 Aligned_cols=59 Identities=25% Similarity=0.529 Sum_probs=46.9
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHh
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLV 123 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll 123 (532)
...|+|.||+|.. .+++...|||.||-.|+-+|+....+ .-.||. |+..++.+.+--|.
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~-----~~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPN-----SKECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCC-----CeeCCc--cccccccceEEeee
Confidence 4679999999984 48999999999999999999988543 246888 88888766554443
No 20
>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=97.64 E-value=4.8e-05 Score=59.23 Aligned_cols=48 Identities=8% Similarity=0.142 Sum_probs=39.3
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHH
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 118 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~ 118 (532)
+.|+||.+.+. +++.++|||.||+.|+..|+.. ...||. |+..++...
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhh
Confidence 57999999866 7888999999999999999975 147988 777665443
No 21
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.63 E-value=0.00037 Score=72.52 Aligned_cols=76 Identities=17% Similarity=0.353 Sum_probs=45.6
Q ss_pred ceeeee-cCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCcceeecCCCC-eeEe-ccCcee
Q 009562 169 VCEVEC-ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN-LVSC-ICGQAF 245 (532)
Q Consensus 169 ~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn-hMtC-~C~~~F 245 (532)
...|.| .|...||.-|...-|.|-.-...++++........ ...-....-.|..+ .|=| .|+| .|+...
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs-~~~s~r~~~~ct~h-------~~e~~smyc~~ck~pv 245 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVS-RRLSPRKVSTCTDH-------ELENHSMYCVQCKMPV 245 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCcee-eccchhhhhhccCC-------CCCCceEEEEecCChH
Confidence 345889 59999999999888887654454554443322110 00000111233322 2223 3999 599999
Q ss_pred ecccccc
Q 009562 246 CWLCGGA 252 (532)
Q Consensus 246 Cw~C~~~ 252 (532)
||.|+.+
T Consensus 246 c~~clee 252 (699)
T KOG4367|consen 246 CYQCLEE 252 (699)
T ss_pred HHHHHHh
Confidence 9999987
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.2e-05 Score=83.61 Aligned_cols=60 Identities=20% Similarity=0.503 Sum_probs=48.0
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhc
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 124 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 124 (532)
...|||||+..+ -+..+.|||.||-.|+-+||...... ....||. |...+...++..+..
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 678999999854 55667899999999999999987332 3589999 999888776665554
No 23
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.59 E-value=5e-05 Score=52.19 Aligned_cols=38 Identities=34% Similarity=0.865 Sum_probs=30.6
Q ss_pred cccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 61 CDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 61 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
|+||++. ...++.++|||.||..|+..|+. .+ ...||.
T Consensus 1 C~iC~~~--~~~~~~~~C~H~~c~~C~~~~~~----~~---~~~CP~ 38 (39)
T smart00184 1 CPICLEE--LKDPVVLPCGHTFCRSCIRKWLK----SG---NNTCPI 38 (39)
T ss_pred CCcCccC--CCCcEEecCCChHHHHHHHHHHH----hC---cCCCCC
Confidence 7899998 34777889999999999999987 12 257875
No 24
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=4.3e-05 Score=76.04 Aligned_cols=52 Identities=29% Similarity=0.653 Sum_probs=42.7
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 119 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i 119 (532)
.....|.+|++... ++..++|||.||..|+.+|...+- .||. |...+.+..+
T Consensus 237 ~a~~kC~LCLe~~~--~pSaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRS--NPSATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCC--CCCcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 34678999999844 888999999999999999998742 3999 9988776543
No 25
>PHA02926 zinc finger-like protein; Provisional
Probab=97.46 E-value=7.7e-05 Score=71.76 Aligned_cols=56 Identities=27% Similarity=0.517 Sum_probs=39.5
Q ss_pred ccccccccccccccc-----ccCce--ecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 55 LSSTVMCDICMEEVA-----GDKAT--KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~-----~~~~~--~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.+...+|+||+|.+- .+..+ ..+|+|.||..|+..|-..+-..| ..-.||. |...+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f 229 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRF 229 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Cccee
Confidence 345689999999852 11122 339999999999999998753322 2357999 88754
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.42 E-value=9.9e-05 Score=78.03 Aligned_cols=66 Identities=23% Similarity=0.544 Sum_probs=47.5
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH-HHHhcCCChhHHHHH
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV-RNLVSKKHPNLAEKF 134 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i-~~ll~~~~~e~~eky 134 (532)
...+.|+||++.+. +++.++|||.||..|+..|+.. ...||. |...+....+ ...+- .++++.|
T Consensus 24 e~~l~C~IC~d~~~--~PvitpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L---~~iVe~~ 88 (397)
T TIGR00599 24 DTSLRCHICKDFFD--VPVLTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLV---SEIVESF 88 (397)
T ss_pred ccccCCCcCchhhh--CccCCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHH---HHHHHHH
Confidence 45789999999875 7778899999999999999864 137998 8887654322 12222 3566666
Q ss_pred HH
Q 009562 135 ER 136 (532)
Q Consensus 135 ~~ 136 (532)
..
T Consensus 89 ~~ 90 (397)
T TIGR00599 89 KN 90 (397)
T ss_pred HH
Confidence 53
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.40 E-value=8.3e-05 Score=74.66 Aligned_cols=45 Identities=29% Similarity=0.812 Sum_probs=38.2
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
.+.+.|+||++.+. ++..++|||.||..|+...+. ..+.||. |..
T Consensus 11 ~~~~~C~iC~~~~~--~p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYFR--EPVLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP 55 (386)
T ss_pred cccccChhhHHHhh--cCccccccchHhHHHHHHhcC--------CCcCCcc--cCC
Confidence 35789999999987 557789999999999999998 2389998 773
No 28
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.36 E-value=0.00013 Score=72.14 Aligned_cols=50 Identities=28% Similarity=0.569 Sum_probs=37.0
Q ss_pred ccccccccccccccccC------ceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 56 SSTVMCDICMEEVAGDK------ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
+...+|+||++.+...+ .+..+|+|.||.+|+..|+.. ...||. |+..+.
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 34679999999865322 234489999999999998753 247999 887553
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.20 E-value=0.00025 Score=71.72 Aligned_cols=64 Identities=22% Similarity=0.582 Sum_probs=50.6
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHH--HhcCCChhHHHH
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRN--LVSKKHPNLAEK 133 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~--ll~~~~~e~~ek 133 (532)
..-..|.||++-|. -++.++|+|.||.-||+.|+.. ...||. |...+.+..++. +|+ |+++-
T Consensus 21 D~lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il~----Eiv~S 84 (442)
T KOG0287|consen 21 DDLLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRILD----EIVKS 84 (442)
T ss_pred HHHHHHhHHHHHhc--CceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHHH----HHHHH
Confidence 34578999999976 6677799999999999999975 367998 998888877653 443 67776
Q ss_pred HH
Q 009562 134 FE 135 (532)
Q Consensus 134 y~ 135 (532)
|.
T Consensus 85 ~~ 86 (442)
T KOG0287|consen 85 LN 86 (442)
T ss_pred HH
Confidence 65
No 30
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=96.80 E-value=0.42 Score=50.81 Aligned_cols=46 Identities=20% Similarity=0.554 Sum_probs=34.9
Q ss_pred cccccccccccccccc--CceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGD--KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
.+..+||||++-.+.+ -..+..|.|.|--.|+..|+. .+||. |...
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~~ 220 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRYC 220 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhhh
Confidence 3567999999987642 234568999999999998865 48988 6643
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=96.68 E-value=0.0011 Score=67.47 Aligned_cols=54 Identities=22% Similarity=0.445 Sum_probs=37.9
Q ss_pred cccccccccccc-cCc--eecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHH
Q 009562 59 VMCDICMEEVAG-DKA--TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRN 121 (532)
Q Consensus 59 ~~C~IC~e~~~~-~~~--~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ 121 (532)
..||||..+... .++ ...+|||.||.+|+...|.. | +..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~---~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G---SGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C---CCCCCC--CCCccchhhccc
Confidence 579999997322 222 11279999999999999742 3 358997 998876665443
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.59 E-value=0.00062 Score=76.05 Aligned_cols=55 Identities=25% Similarity=0.682 Sum_probs=45.3
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNL 122 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~l 122 (532)
...+|++|.+- ..+.+...|||.||.+|++..+.+. .=+||. |+..|...+|..+
T Consensus 642 ~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETR-------QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHh-------cCCCCC--CCCCCCccccccc
Confidence 56799999954 4478888999999999999999884 358998 9999988777653
No 33
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.50 E-value=0.0019 Score=49.72 Aligned_cols=47 Identities=23% Similarity=0.508 Sum_probs=31.1
Q ss_pred cccccccccccccccCcee-cCCCCcccHHHHHHHHHhhhccCCcccccccccccc
Q 009562 57 STVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 111 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 111 (532)
..+.|||....+. +|+. ..|||.|.++.+.+|+.. ...++||..+|.
T Consensus 10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~------~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQR------NGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTT------TS-EE-SCCC-S
T ss_pred eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHh------cCCCCCCCCCCC
Confidence 4688999999866 6665 599999999999999921 245899999985
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=96.41 E-value=0.0021 Score=52.01 Aligned_cols=50 Identities=12% Similarity=0.107 Sum_probs=37.6
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 117 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~ 117 (532)
+.|.|+|+.+.+. +++.+++||.|++.+|..|+.. ....||. |+..+...
T Consensus 3 ~~f~CpIt~~lM~--dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELMR--DPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB-S--SEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHhh--CceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcc
Confidence 5799999999966 9999999999999999999986 2357888 66666553
No 35
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.21 E-value=0.00078 Score=52.49 Aligned_cols=43 Identities=23% Similarity=0.719 Sum_probs=22.1
Q ss_pred ccccccccccccccCceec-CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 58 TVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
-..|++|.+.+. +++.+ .|.|.||..|+...+. ..||. |..+-
T Consensus 7 lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPA 50 (65)
T ss_dssp TTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-
T ss_pred hcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC----------CCCCC--cCChH
Confidence 457999999865 78776 9999999999976433 25998 77654
No 36
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.005 Score=61.76 Aligned_cols=52 Identities=23% Similarity=0.536 Sum_probs=42.0
Q ss_pred ccccccccccccccc-cCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 56 SSTVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
....+|.||++.+.. +....++|.|.|...|+..|+.. ....||. |+..+++
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 345799999999754 44566799999999999999874 3468998 9988764
No 37
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.95 E-value=0.0034 Score=67.03 Aligned_cols=55 Identities=20% Similarity=0.502 Sum_probs=44.3
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChH
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 117 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~ 117 (532)
.....|.+|-++ .++.+...|.|.||+-|+++|+....... .+.||. |...++.+
T Consensus 534 k~~~~C~lc~d~--aed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 534 KGEVECGLCHDP--AEDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred cCceeecccCCh--hhhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 456799999988 44888889999999999999999876543 389998 88766444
No 38
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0047 Score=61.07 Aligned_cols=53 Identities=30% Similarity=0.568 Sum_probs=41.0
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 119 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i 119 (532)
..+.|.||++. ...+..++|||.||..|+-..|..+ ..-.||. |.+.+.+..|
T Consensus 214 ~d~kC~lC~e~--~~~ps~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEE--PEVPSCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeecc--cCCcccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 46889999998 4478888999999999999965542 2235998 8887765554
No 39
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.87 E-value=0.0045 Score=64.17 Aligned_cols=45 Identities=24% Similarity=0.595 Sum_probs=37.1
Q ss_pred cccccccccccccC-ceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 59 VMCDICMEEVAGDK-ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 59 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
.+|.||+|++...+ ...|+|.|.|...|+..|+... .-.||. |+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-------CccCCC--CCC
Confidence 69999999987654 5567999999999999999873 246999 665
No 40
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.73 E-value=0.0089 Score=43.14 Aligned_cols=33 Identities=24% Similarity=0.427 Sum_probs=28.4
Q ss_pred CccccCCHHHHHHHHHHcCCChHHHHHHHHhcC
Q 009562 1 MELLSLREHHARTLLIHYRWDVEKLLAVLVENG 33 (532)
Q Consensus 1 ~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~ 33 (532)
|+|.|++++.|+.+|..++||++..++.|++.+
T Consensus 8 ~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 8 MSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred HHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 568899999999999999999999999999754
No 41
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=95.63 E-value=0.0075 Score=48.77 Aligned_cols=41 Identities=24% Similarity=0.495 Sum_probs=29.1
Q ss_pred cccccccccccc----------cCcee-cCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 59 VMCDICMEEVAG----------DKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 59 ~~C~IC~e~~~~----------~~~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
..|.||++.+.. +-++. ..|||.|...|+.+++... -.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC
Confidence 359999999821 12223 3899999999999999652 28887
No 42
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.99 E-value=0.014 Score=58.20 Aligned_cols=49 Identities=29% Similarity=0.602 Sum_probs=38.4
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
....-|-||-+-+. -+...+|||.||.-||+.|+.+ ..-||. |....-+
T Consensus 23 Ds~lrC~IC~~~i~--ip~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~e 71 (391)
T COG5432 23 DSMLRCRICDCRIS--IPCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCE 71 (391)
T ss_pred hhHHHhhhhhheee--cceecccccchhHHHHHHHhcC--------CCCCcc--ccccHHh
Confidence 34678999988866 5677799999999999999975 257888 7765433
No 43
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.024 Score=56.36 Aligned_cols=51 Identities=22% Similarity=0.541 Sum_probs=38.9
Q ss_pred cccccccccccccccccCceec-CCCCcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 55 LSSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
.+...+|++|.+. +.-|..+ +|||.||--|+..-+... ..+.||. |+..+.
T Consensus 236 ~t~~~~C~~Cg~~--PtiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEP--PTIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCC--CCCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 4567899999887 3355555 699999999999876652 3489998 887665
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.47 E-value=0.018 Score=46.20 Aligned_cols=57 Identities=25% Similarity=0.408 Sum_probs=26.6
Q ss_pred cccccccccccc-ccCc-ee----cCCCCcccHHHHHHHHHhhhccCCcc-cc--cccccccccccCh
Q 009562 58 TVMCDICMEEVA-GDKA-TK----MDCGHCFCNDCWTEHFIVKINEGQSK-RI--RCMAHKCNAICDE 116 (532)
Q Consensus 58 ~~~C~IC~e~~~-~~~~-~~----l~CgH~fC~~C~~~yl~~~i~~g~~~-~i--~CP~~~C~~~~~~ 116 (532)
...|+||+..+. .+.. .. ..|+..|...|+.+||...-...+.+ ++ .||. |...+..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 468999999754 2222 21 26899999999999998766544332 22 6998 8887643
No 45
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.30 E-value=0.024 Score=57.12 Aligned_cols=54 Identities=22% Similarity=0.492 Sum_probs=41.4
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHH
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 120 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 120 (532)
....+|.||+.+ ...++.|+|+|.||.-|++.-+.. +. -.|+. |...++...+.
T Consensus 5 ~~~~eC~IC~nt--~n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 5 TKKKECLICYNT--GNCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred ccCCcceeeecc--CCcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchhc
Confidence 345689999998 347799999999999999886543 22 35998 99888776543
No 46
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.09 E-value=0.068 Score=56.90 Aligned_cols=49 Identities=24% Similarity=0.595 Sum_probs=38.4
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
...|.|.||+..+. ++++++|||.||..|+..-+. ....||. |...+..
T Consensus 82 ~sef~c~vc~~~l~--~pv~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY--PPVVTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC--CCccccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 46799999999876 788889999999999776322 2357887 8877654
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.27 E-value=0.063 Score=39.69 Aligned_cols=44 Identities=30% Similarity=0.708 Sum_probs=21.4
Q ss_pred cccccccccccC--ceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 61 CDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 61 C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
|++|.++++..+ +...+||+.+|..||..-... .+ =+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~~----g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---EG----GRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S-----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---cC----CCCCC--CCCC
Confidence 789999875433 344589999999999886652 12 37988 8754
No 48
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.11 E-value=0.082 Score=56.35 Aligned_cols=138 Identities=22% Similarity=0.421 Sum_probs=77.0
Q ss_pred cCCHHHHHHHHHHcCCChHHHHHHHHhcCchhhhhhhCCcccCCCCCCCCccccccccccccccccc---Cce---ecCC
Q 009562 5 SLREHHARTLLIHYRWDVEKLLAVLVENGKESLFNEAGVTVIDDADPMLPLSSTVMCDICMEEVAGD---KAT---KMDC 78 (532)
Q Consensus 5 ~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~C~IC~e~~~~~---~~~---~l~C 78 (532)
.++......||-- +|.+.|...-.+.+........ . ....|+.|....... ... -..|
T Consensus 201 ~l~~~~c~~llt~------kl~e~~e~~~~e~~i~~~~~~y-----c-----p~~~C~~l~~~~el~~~~~~~~~~C~~C 264 (384)
T KOG1812|consen 201 RLTLESCRKLLTP------KLREMWEQRLKEEVIPSLDRVY-----C-----PYPRCSSLMSKTELSSEVKSKRRPCVKC 264 (384)
T ss_pred cCCHHHHhhhcCH------HHHHHHHHHHHHHhhhhhhccc-----C-----CCCCchHhhhhhhhccchhhcccccccC
Confidence 4566677777743 5555554322222222221110 0 134577777653321 121 2378
Q ss_pred CCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhcCCChhHHHHHHHHHHHHhhhcccccccCCCCCCC
Q 009562 79 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHC 158 (532)
Q Consensus 79 gH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C 158 (532)
+-.||.+|-..|-. ++.| +.++++.+. + +.......++. ...+.|| .|
T Consensus 265 ~~~fCv~C~~~wh~---------~~sC-----------~eykk~~~~---~----~~d~~~~~~la--~~wr~Cp---kC 312 (384)
T KOG1812|consen 265 HELFCVKCKVPWHA---------NLSC-----------EEYKKLNPE---E----YVDDITLKYLA--KRWRQCP---KC 312 (384)
T ss_pred CCceeecCCCcCCC---------CCCH-----------HHHHHhCCc---c----cccHHHHHHHH--HhcCcCc---cc
Confidence 88899988555422 2344 455665541 1 11112222333 4567898 79
Q ss_pred CceEEeccccceeeeecCCCeeecCcccCCCCC
Q 009562 159 GNAIRVEEVEVCEVECACGAQFCFSCLSEAHSP 191 (532)
Q Consensus 159 ~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p 191 (532)
...|..... ...++|.||+.||..|+.+|+..
T Consensus 313 ~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 313 KFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred ceeeeecCC-cceEEeeccccchhhcCcchhhC
Confidence 988875544 66789999999999999888654
No 49
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=93.08 E-value=0.07 Score=55.16 Aligned_cols=49 Identities=27% Similarity=0.623 Sum_probs=37.9
Q ss_pred cccccccccccc-cccc----------CceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 56 SSTVMCDICMEE-VAGD----------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 56 ~~~~~C~IC~e~-~~~~----------~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.....|.||.|+ +... .+-.++|||.+...|++.|++.+ -.||. |+.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCcc
Confidence 346789999999 4322 24578999999999999999852 47998 87653
No 50
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.98 E-value=0.034 Score=52.64 Aligned_cols=32 Identities=28% Similarity=0.816 Sum_probs=27.6
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEH 90 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 90 (532)
.+|.|.||-.++. .++...|||.||..|...-
T Consensus 195 IPF~C~iCKkdy~--spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 195 IPFLCGICKKDYE--SPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred Cceeehhchhhcc--chhhhhcchhHHHHHHHHH
Confidence 4689999999987 7888899999999996553
No 51
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.55 E-value=0.026 Score=58.08 Aligned_cols=49 Identities=29% Similarity=0.646 Sum_probs=35.9
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
...+.|+||++-+. .-+....|+|+||.+||..-+.. |. -.||. |...+
T Consensus 41 ~~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS----GN---NECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhhc
Confidence 35789999999876 23556699999999998765543 32 47887 77543
No 52
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=92.39 E-value=0.21 Score=59.41 Aligned_cols=66 Identities=24% Similarity=0.506 Sum_probs=53.4
Q ss_pred ccccccccccc-ccccCceecCCCCcccHHHHHHHHHhhhccCC--cccccccccccccccChHHHHHHhc
Q 009562 57 STVMCDICMEE-VAGDKATKMDCGHCFCNDCWTEHFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVS 124 (532)
Q Consensus 57 ~~~~C~IC~e~-~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~ 124 (532)
..-.|.|||.+ +.....+.+.|+|.|...|.+.-++..-.... +..|.||. |+..+....++.++.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLld 3553 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLD 3553 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHH
Confidence 34579999988 55567788999999999999999887665433 24589999 999998888888886
No 53
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=92.15 E-value=0.4 Score=48.75 Aligned_cols=147 Identities=20% Similarity=0.386 Sum_probs=78.3
Q ss_pred HHHHHcCCChHHHHHHHHhcCchhh-hhhhCCcccCCCCCCCCcccccccccccccccccCceec--CCCCcccHHHHHH
Q 009562 13 TLLIHYRWDVEKLLAVLVENGKESL-FNEAGVTVIDDADPMLPLSSTVMCDICMEEVAGDKATKM--DCGHCFCNDCWTE 89 (532)
Q Consensus 13 ~LL~~~~W~~~~l~~~~~~~~~~~~-~~~~gl~~~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~C~~~ 89 (532)
.=|.||+-=-+.-++.|.....|+. +..-|+.-+.+. |..=+-.-+...-++. .||-.||+.|+..
T Consensus 285 ~e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pg-----------CG~gll~EPD~rkvtC~~gCgf~FCR~C~e~ 353 (446)
T KOG0006|consen 285 KELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPG-----------CGAGLLPEPDQRKVTCEGGCGFAFCRECKEA 353 (446)
T ss_pred HhhhhheecchhHHHHHHHhhhhhheeecCCEecCCCC-----------CCcccccCCCCCcccCCCCchhHhHHHHHhh
Confidence 4467888888888888876555444 333344322211 1111111011111222 4999999999999
Q ss_pred HHHhhhccCC--cccccccccccccccChHHHHHHhcCCChhHHHHHHHHHHHHhhhcccccccCCCCCCCCceEEeccc
Q 009562 90 HFIVKINEGQ--SKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEV 167 (532)
Q Consensus 90 yl~~~i~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~ 167 (532)
|-...-..+. +..- .|...+++... ...+|+...-. ......+.|| .|......++
T Consensus 354 yh~geC~~~~~as~t~-----tc~y~vde~~a----------~~arwd~as~~---TIk~tTkpCP---kChvptErnG- 411 (446)
T KOG0006|consen 354 YHEGECSAVFEASGTT-----TCAYRVDERAA----------EQARWDAASKE---TIKKTTKPCP---KCHVPTERNG- 411 (446)
T ss_pred hccccceeeecccccc-----ceeeecChhhh----------hhhhhhhhhhh---hhhhccCCCC---CccCccccCC-
Confidence 8653222111 0111 24434433221 12344433221 1223567888 6876665433
Q ss_pred cceeeee--c-CCCeeecCcccCCCCCC
Q 009562 168 EVCEVEC--A-CGAQFCFSCLSEAHSPC 192 (532)
Q Consensus 168 ~~~~v~C--~-C~~~fC~~C~~~~H~p~ 192 (532)
....+.| + ||..+||.|+.+|...+
T Consensus 412 GCmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 412 GCMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred ceEEeecCCCCCCceeEeccCChhhhhh
Confidence 3456789 3 99999999999987643
No 54
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=92.04 E-value=0.1 Score=53.47 Aligned_cols=46 Identities=24% Similarity=0.643 Sum_probs=35.8
Q ss_pred cccccccccccccccCcee-cCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 57 STVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
...+|.+|-.-+- +..+ ..|-|.||+.||-.|+.. .-.||. |...+
T Consensus 14 ~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVI 60 (331)
T ss_pred cceehhhccceee--cchhHHHHHHHHHHHHHHHHHHH--------hccCCc--cceec
Confidence 3679999987754 4444 489999999999999997 257998 66544
No 55
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.00 E-value=0.1 Score=54.46 Aligned_cols=56 Identities=25% Similarity=0.469 Sum_probs=37.5
Q ss_pred cccccccccccccccccC-----cee-cCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 55 LSSTVMCDICMEEVAGDK-----ATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
.+...+|.||++.+.... .-. .+|.|.||..|++.|=...-. +....-.||. |...
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~ 219 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVP 219 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCc
Confidence 456789999999965322 222 379999999999998643211 2223457998 7753
No 56
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.12 E-value=0.24 Score=52.05 Aligned_cols=38 Identities=37% Similarity=0.797 Sum_probs=34.4
Q ss_pred cCccCCCC--CCcceeecCCCCeeEe-ccCceeeccccccc
Q 009562 216 VHTKPCPK--CHKPVEKNGGCNLVSC-ICGQAFCWLCGGAT 253 (532)
Q Consensus 216 ~~tK~CPk--C~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~ 253 (532)
.+..-||+ |..|+-...|++-..| +|.+.||.+|...|
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~ 311 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTW 311 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhh
Confidence 46789999 9999977889999999 69999999999885
No 57
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.02 E-value=0.23 Score=55.51 Aligned_cols=45 Identities=29% Similarity=0.791 Sum_probs=36.2
Q ss_pred cccccccccccccc-C--ceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 58 TVMCDICMEEVAGD-K--ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 58 ~~~C~IC~e~~~~~-~--~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
...|.||.|++... . +..++|+|.||..|++.|++. .-.||. |+.
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 57899999996521 1 567899999999999999997 247998 655
No 58
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.72 E-value=0.32 Score=49.86 Aligned_cols=56 Identities=27% Similarity=0.656 Sum_probs=41.3
Q ss_pred ccccccccccccccC----ceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccc--cChHHHHHH
Q 009562 58 TVMCDICMEEVAGDK----ATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI--CDEAVVRNL 122 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~----~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~--~~~~~i~~l 122 (532)
...|.||-++++..+ |..+.|||.+|..|....+.. ..+.||. |... ++...++.+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSL 64 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhh
Confidence 357999999987542 456789999999999988765 3477877 8876 555555544
No 59
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.71 E-value=0.17 Score=53.11 Aligned_cols=49 Identities=22% Similarity=0.687 Sum_probs=37.8
Q ss_pred ccccccccccccc---cCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 58 TVMCDICMEEVAG---DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 58 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
..+||||++.+.. ..++++.|||-|=.+|+..|+. + .....||. |...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k-----~~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-K-----KTKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-h-----hhhhhCcc--cCChh
Confidence 4689999999542 3467789999999999999993 2 24578998 77543
No 60
>PRK00420 hypothetical protein; Validated
Probab=90.53 E-value=2.1 Score=37.55 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=20.6
Q ss_pred ccCCCCCCcceeecCCCCeeEeccCceeecccccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 252 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~ 252 (532)
...||.|+.|+-+. +-|..||-.|+..
T Consensus 23 ~~~CP~Cg~pLf~l--------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL--------KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec--------CCCceECCCCCCe
Confidence 37999999998741 3457888888876
No 61
>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=89.77 E-value=0.15 Score=32.75 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=15.0
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCcee
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 245 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~F 245 (532)
|.||.|+..|-.+ -..|. ||+.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5788888888522 15564 77765
No 62
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=89.59 E-value=0.3 Score=40.58 Aligned_cols=31 Identities=19% Similarity=0.498 Sum_probs=24.9
Q ss_pred CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 77 DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 77 ~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.|+|.|...||..++.++-. .-.||. |...+
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w 81 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPW 81 (85)
T ss_pred cCccHHHHHHHHHHHccccC-----CCCCCC--cCCee
Confidence 79999999999999997521 247998 88754
No 63
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.49 E-value=0.23 Score=51.16 Aligned_cols=52 Identities=31% Similarity=0.620 Sum_probs=37.8
Q ss_pred CCcccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 53 LPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 53 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
.|.++...|+||+-. +-..+..+|+|.-|.+|+.+|+.. .-+|-. |+..+..
T Consensus 417 lp~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVID 468 (489)
T ss_pred CCCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhc--------CCeeeE--ecceeee
Confidence 345677899999975 223455699999999999999864 135766 8876543
No 64
>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=89.11 E-value=10 Score=39.16 Aligned_cols=52 Identities=29% Similarity=0.680 Sum_probs=34.1
Q ss_pred cCCCCCCCCceEEeccccceeeeecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCcceee
Q 009562 151 WCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEK 230 (532)
Q Consensus 151 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEK 230 (532)
-|| -|..-..........+. +|||.||.+|.... | ..+..+||.|+.++.+
T Consensus 5 ~CP---~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----------~--------------~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCP---RCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----------F--------------VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCC---cCCCCCccCcccccccC-CCCCcccHHHHHHH-----------h--------------cCCCCCCCCCCCccch
Confidence 477 57765554444444455 89999999996531 1 1123589999999885
Q ss_pred c
Q 009562 231 N 231 (532)
Q Consensus 231 n 231 (532)
+
T Consensus 56 ~ 56 (309)
T TIGR00570 56 N 56 (309)
T ss_pred h
Confidence 4
No 65
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.72 E-value=0.23 Score=49.36 Aligned_cols=53 Identities=28% Similarity=0.617 Sum_probs=40.4
Q ss_pred ccccccccccccccc--------CceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChH
Q 009562 57 STVMCDICMEEVAGD--------KATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 117 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~ 117 (532)
+...|.||...+..+ +...++|+|.|...|++.|... | ..-.||- |++.++..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----G--KkqtCPY--CKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----G--KKQTCPY--CKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----c--CCCCCch--HHHHhhHh
Confidence 356799998875432 4678999999999999999875 2 2358998 99877543
No 66
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=88.62 E-value=0.42 Score=35.51 Aligned_cols=42 Identities=17% Similarity=0.377 Sum_probs=31.6
Q ss_pred ccccccccccccCceecCCC-----CcccHHHHHHHHHhhhccCCcccccccc
Q 009562 60 MCDICMEEVAGDKATKMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 60 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
.|-||++....+++...||. |.+..+|+..|+..+- ..+||.
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 38899984444566677885 8899999999998742 247876
No 67
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=88.35 E-value=0.2 Score=45.08 Aligned_cols=34 Identities=32% Similarity=0.703 Sum_probs=28.0
Q ss_pred ccccccccccccc-cCceecCCC------CcccHHHHHHHH
Q 009562 58 TVMCDICMEEVAG-DKATKMDCG------HCFCNDCWTEHF 91 (532)
Q Consensus 58 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~yl 91 (532)
..+|.||++.+.. +-++.++|| |.||.+|++.|=
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 6799999999876 345667787 789999999983
No 68
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.45 E-value=0.52 Score=48.91 Aligned_cols=48 Identities=23% Similarity=0.535 Sum_probs=36.8
Q ss_pred ccccccccccccccccCceecCCCCc-ccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
+...+|.||+.+.. +.+.|+|.|. .|.+|-+..-- . .=.||. |...+.
T Consensus 288 ~~gkeCVIClse~r--dt~vLPCRHLCLCs~Ca~~Lr~---q-----~n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESR--DTVVLPCRHLCLCSGCAKSLRY---Q-----TNNCPI--CRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCc--ceEEecchhhehhHhHHHHHHH---h-----hcCCCc--cccchH
Confidence 44679999999944 8899999997 89999776541 1 136999 987653
No 69
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=87.10 E-value=0.93 Score=46.48 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=36.6
Q ss_pred ccccccccccccccccCceec-CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.....|+||+.... ++..+ --|-.||-.|+-.|+.. .| +||..+|+..+
T Consensus 298 ~~~~~CpvClk~r~--Nptvl~vSGyVfCY~Ci~~Yv~~---~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQ--NPTVLEVSGYVFCYPCIFSYVVN---YG-----HCPVTGYPASV 347 (357)
T ss_pred CccccChhHHhccC--CCceEEecceEEeHHHHHHHHHh---cC-----CCCccCCcchH
Confidence 35678999998744 44444 56999999999999983 22 69988887644
No 70
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.67 E-value=0.41 Score=51.36 Aligned_cols=51 Identities=22% Similarity=0.414 Sum_probs=37.1
Q ss_pred cccccccccccccccc-----Cc----------eecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 56 SSTVMCDICMEEVAGD-----KA----------TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~-----~~----------~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
.....|.||+.+++.- .+ ...+|.|.|...|+.+|+++ ..+.||. |...++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCC
Confidence 4567899999987621 11 12399999999999999985 2378998 665554
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=85.54 E-value=0.22 Score=48.64 Aligned_cols=49 Identities=20% Similarity=0.493 Sum_probs=36.2
Q ss_pred cccccccccccc-cCceec---CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 59 VMCDICMEEVAG-DKATKM---DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 59 ~~C~IC~e~~~~-~~~~~l---~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
-.||||-.+.-. -++..+ .|-|..|-+|...-|.. .+-.||-++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence 469999988322 233333 49999999999988865 35789999998654
No 72
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=83.89 E-value=0.52 Score=49.30 Aligned_cols=45 Identities=31% Similarity=0.752 Sum_probs=33.4
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccc
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCN 111 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~ 111 (532)
..|-||-|.- .++-.-+|||..|..|+..|=.. .+|+ .||.+.|.
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcE 414 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCE 414 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhccc--CCCC----CCCceeeE
Confidence 3699999873 35556699999999999998544 2355 79985554
No 73
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=83.86 E-value=0.46 Score=54.19 Aligned_cols=48 Identities=29% Similarity=0.644 Sum_probs=36.9
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChH
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEA 117 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~ 117 (532)
+.|.||.+ .+.++...|+|.||.+||..++...-. -.||. |...+...
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKEK 502 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC------CCCcH--HHHHHHHH
Confidence 89999999 457788899999999999999876321 26776 77655443
No 74
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.78 E-value=0.38 Score=36.31 Aligned_cols=45 Identities=27% Similarity=0.476 Sum_probs=32.7
Q ss_pred cccccccccccccCceecCCCCc-ccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 59 VMCDICMEEVAGDKATKMDCGHC-FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
-+|.||+|. +-+.+.-.|||. .|.+|-.+.+.. .. =.||. |..++
T Consensus 8 dECTICye~--pvdsVlYtCGHMCmCy~Cg~rl~~~--~~-----g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEH--PVDSVLYTCGHMCMCYACGLRLKKA--LH-----GCCPI--CRAPI 53 (62)
T ss_pred cceeeeccC--cchHHHHHcchHHhHHHHHHHHHHc--cC-----CcCcc--hhhHH
Confidence 689999997 224445589998 899998888775 22 36888 77654
No 75
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.69 E-value=0.87 Score=51.48 Aligned_cols=39 Identities=10% Similarity=0.089 Sum_probs=21.5
Q ss_pred ccccccccccccc-cC-ceec---CCCCcccHHHHHHHHHhhhc
Q 009562 58 TVMCDICMEEVAG-DK-ATKM---DCGHCFCNDCWTEHFIVKIN 96 (532)
Q Consensus 58 ~~~C~IC~e~~~~-~~-~~~l---~CgH~fC~~C~~~yl~~~i~ 96 (532)
..+|.||.-++.. .+ .-.+ .|+|.+|-.||..+...-+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 4455565555432 11 1122 37777777777777666553
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=81.95 E-value=1.2 Score=32.94 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=19.8
Q ss_pred cCCCCCCcceeecC--CCCeeEec-cCcee
Q 009562 219 KPCPKCHKPVEKNG--GCNLVSCI-CGQAF 245 (532)
Q Consensus 219 K~CPkC~~~IEKn~--GCnhMtC~-C~~~F 245 (532)
+.||.|+.++.... +-+++.|. ||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 36999999887543 35688995 99763
No 77
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.72 E-value=0.64 Score=47.01 Aligned_cols=45 Identities=27% Similarity=0.691 Sum_probs=35.1
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
+|-|.||-..+- +++...|+|.||..|....+.. | -+|+. |....
T Consensus 241 Pf~c~icr~~f~--~pVvt~c~h~fc~~ca~~~~qk----~----~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVVTKCGHYFCEVCALKPYQK----G----EKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccc--cchhhcCCceeehhhhcccccc----C----Cccee--ccccc
Confidence 578999999976 8889999999999997765542 2 46777 77543
No 78
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=80.25 E-value=0.48 Score=46.65 Aligned_cols=45 Identities=24% Similarity=0.549 Sum_probs=32.2
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
+.|..|+---+...++.+.|+|.||..|.+.- .+-.||. |+..+.
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir 48 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSIR 48 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccC----------Ccccccc--ccceee
Confidence 56998987655445556699999999996542 2228998 887653
No 79
>PHA00626 hypothetical protein
Probab=79.83 E-value=1.4 Score=33.46 Aligned_cols=28 Identities=29% Similarity=0.578 Sum_probs=20.7
Q ss_pred CCCCCCc-ceeecCCCCe----eEec-cCceeec
Q 009562 220 PCPKCHK-PVEKNGGCNL----VSCI-CGQAFCW 247 (532)
Q Consensus 220 ~CPkC~~-~IEKn~GCnh----MtC~-C~~~FCw 247 (532)
.||+|+. -|-|++-|+. ..|+ ||+.|=-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 6999999 4878777654 6774 8877744
No 80
>PF04641 Rtf2: Rtf2 RING-finger
Probab=79.29 E-value=1.5 Score=44.21 Aligned_cols=59 Identities=20% Similarity=0.389 Sum_probs=43.7
Q ss_pred ccccccccccccccccc-Cceec-CCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhc
Q 009562 55 LSSTVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVS 124 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 124 (532)
....+.|||...++... .++.+ +|||+|+..++.+.= .+ -.||. |...+...+|-.|.+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNP 170 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecC
Confidence 35679999999998643 34445 999999999999871 11 35998 999887776655554
No 81
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.99 E-value=1.2 Score=48.45 Aligned_cols=46 Identities=35% Similarity=0.671 Sum_probs=36.1
Q ss_pred ccCCC--CCCcceee-cCCCCeeEeccCceeecccccccCCCCCccccCCccccCcc
Q 009562 218 TKPCP--KCHKPVEK-NGGCNLVSCICGQAFCWLCGGATGRDHTWSRIAGHSCGRYK 271 (532)
Q Consensus 218 tK~CP--kC~~~IEK-n~GCnhMtC~C~~~FCw~C~~~~~~~H~w~~h~g~~C~~~~ 271 (532)
.|-|| .|+..+.- .+.+.-+.|.|++.|||.|+.+| |.+-+|.-..
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~--------H~p~~C~~~~ 206 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEES--------HSPVSCPGAK 206 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccc--------cCCCcccchH
Confidence 46665 59998887 88899999999999999999885 3444666544
No 82
>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=78.63 E-value=55 Score=37.99 Aligned_cols=48 Identities=13% Similarity=0.240 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHH
Q 009562 374 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVIT 422 (532)
Q Consensus 374 ~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~ 422 (532)
+.+-..+.|+.|++.++.|...+......++..| .+++.++..+...+
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AE-r~~~~EL~~~~~~l 648 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAE-REFKKELERMKDQL 648 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHH-HHHHHHHHHHHHHH
Confidence 5567778899999999999999987666666544 44444444444443
No 83
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.76 E-value=1.3 Score=43.58 Aligned_cols=54 Identities=9% Similarity=0.230 Sum_probs=39.4
Q ss_pred cccccccccccccccc-Cceec-CCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH
Q 009562 56 SSTVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 119 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i 119 (532)
+..+.|+||-++++.. ....| +|||.||.+|....|.. ...||. |...+.+.+|
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdi 274 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDI 274 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccce
Confidence 3568899999997642 23334 99999999999988764 256777 7766666554
No 84
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.36 E-value=0.95 Score=47.36 Aligned_cols=49 Identities=27% Similarity=0.625 Sum_probs=34.5
Q ss_pred cccccccccccccc-Cceec-CCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 58 TVMCDICMEEVAGD-KATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 58 ~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
...|.||-+-++.. +...+ .|||.|...|+.+|+...-.. -.||. |...
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ik 54 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQIK 54 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eeec
Confidence 45799996655543 34455 499999999999999874332 35887 6633
No 85
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.19 E-value=1.3 Score=43.51 Aligned_cols=47 Identities=32% Similarity=0.808 Sum_probs=28.8
Q ss_pred CCCceEEeccccceeeeecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 157 HCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 157 ~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
+|+ |..+....+.|+| ||+.|||-|... |.. +..+.+.||-|+..|.
T Consensus 49 dCN--ICLd~akdPVvTl-CGHLFCWpClyq------------Wl~-----------~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 49 DCN--ICLDLAKDPVVTL-CGHLFCWPCLYQ------------WLQ-----------TRPNSKECPVCKAEVS 95 (230)
T ss_pred eee--eeccccCCCEEee-cccceehHHHHH------------HHh-----------hcCCCeeCCccccccc
Confidence 454 3333333333444 999999999764 332 1234578999998776
No 86
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=77.05 E-value=1.1 Score=47.86 Aligned_cols=47 Identities=30% Similarity=0.795 Sum_probs=36.6
Q ss_pred cccccccccccccccccCcee-cCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 55 LSSTVMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
......|++|...+. +++. ..|||.||..|+..+... ...||. |...
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~ 65 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQE 65 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc--------CcCCcc--cccc
Confidence 345689999999876 6676 599999999999998775 257776 5443
No 87
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.01 E-value=2.2 Score=44.94 Aligned_cols=57 Identities=18% Similarity=0.398 Sum_probs=40.9
Q ss_pred cccccccccccccc-cCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHH
Q 009562 57 STVMCDICMEEVAG-DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 120 (532)
Q Consensus 57 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 120 (532)
+.|.|||=-+.-+. +.|..|.|||..|++=+..... +|. ..++||- |+..-.....+
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~-~sfKCPY--CP~e~~~~~~k 390 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGS-QSFKCPY--CPVEQLASDTK 390 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCC-eeeeCCC--CCcccCHHhcc
Confidence 46899998776443 4577889999999998777644 343 4789998 88765544433
No 88
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=75.85 E-value=1.7 Score=31.38 Aligned_cols=30 Identities=33% Similarity=0.604 Sum_probs=23.0
Q ss_pred HHHHcCccCCCCCCcceeecCCCCeeEec---cCcee
Q 009562 212 NWITVHTKPCPKCHKPVEKNGGCNLVSCI---CGQAF 245 (532)
Q Consensus 212 ~~i~~~tK~CPkC~~~IEKn~GCnhMtC~---C~~~F 245 (532)
.|.....+.||+|+..- |+--+.|+ |++.|
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 35667789999999875 77778883 77655
No 89
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.39 E-value=1.8 Score=49.28 Aligned_cols=25 Identities=48% Similarity=1.056 Sum_probs=16.1
Q ss_pred cCCCCCCcceeecCCCCeeEeccCceeecccccccC
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATG 254 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~~ 254 (532)
+.||+|+..+. =+..||-.||...+
T Consensus 28 ~~Cp~CG~~~~-----------~~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTEVP-----------VDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCCCC-----------cccccccccCCccc
Confidence 45777776654 23458888887643
No 90
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=74.15 E-value=3.9 Score=41.46 Aligned_cols=48 Identities=25% Similarity=0.646 Sum_probs=33.5
Q ss_pred ccccccccc-cccCceec--CCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 60 MCDICMEEV-AGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 60 ~C~IC~e~~-~~~~~~~l--~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
.||+|-.+. -.-+++.+ +|+|..|.+|+-.-+.. .+-.||. |..++..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cpe--C~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCPE--CMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCCc--ccchhhh
Confidence 489998773 22233333 89999999999988765 2367984 9876543
No 91
>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=74.11 E-value=2.3 Score=30.02 Aligned_cols=27 Identities=22% Similarity=0.700 Sum_probs=23.4
Q ss_pred cCCCCCCcc-eeecCCCCeeEec-cCceeecccccc
Q 009562 219 KPCPKCHKP-VEKNGGCNLVSCI-CGQAFCWLCGGA 252 (532)
Q Consensus 219 K~CPkC~~~-IEKn~GCnhMtC~-C~~~FCw~C~~~ 252 (532)
..|+.|... +. ++|. |+..+|..|...
T Consensus 4 ~~C~~H~~~~~~-------~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSBEE-------EEETTTTEEEEHHHHHT
T ss_pred ccCccCCccceE-------EEecCCCCccCccCCCC
Confidence 689999988 88 9995 999999999987
No 92
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.70 E-value=1.8 Score=27.63 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=8.6
Q ss_pred cCCCCCCccee
Q 009562 219 KPCPKCHKPVE 229 (532)
Q Consensus 219 K~CPkC~~~IE 229 (532)
+.||+|+..|+
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 67888888765
No 93
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.49 E-value=1.8 Score=26.90 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.7
Q ss_pred CCCCCCccee
Q 009562 220 PCPKCHKPVE 229 (532)
Q Consensus 220 ~CPkC~~~IE 229 (532)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 3788888886
No 94
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=73.44 E-value=2.4 Score=48.62 Aligned_cols=51 Identities=25% Similarity=0.438 Sum_probs=39.4
Q ss_pred ccccccccccccccccC-ceec-CCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 56 SSTVMCDICMEEVAGDK-ATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
...++|.||++.+.... +.+. .|-|.|-..||+.|....-.+|. ...+||.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~ 241 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA 241 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc
Confidence 45789999999987544 4444 78999999999999988555544 5678886
No 95
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=73.25 E-value=2.2 Score=31.92 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=20.0
Q ss_pred cCccCCCCCCc-ceeecCCCCeeEe-ccCcee
Q 009562 216 VHTKPCPKCHK-PVEKNGGCNLVSC-ICGQAF 245 (532)
Q Consensus 216 ~~tK~CPkC~~-~IEKn~GCnhMtC-~C~~~F 245 (532)
...+.||+|+. .+.... +.++| +||+.+
T Consensus 18 ~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred EccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 34579999998 444333 68999 599875
No 96
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=72.97 E-value=1.6 Score=44.80 Aligned_cols=54 Identities=26% Similarity=0.553 Sum_probs=38.4
Q ss_pred ccccccccccccc--cCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHH
Q 009562 58 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVR 120 (532)
Q Consensus 58 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 120 (532)
.-.|+.|.++++. .+++..+||-..|.-||... ...+ .=+||. |....+++.|+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~l------ngrcpa--crr~y~denv~ 69 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNL------NGRCPA--CRRKYDDENVR 69 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhc------cCCChH--hhhhcccccee
Confidence 3459999999654 45677799999999999763 3222 347998 88766555443
No 97
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=72.80 E-value=8.6 Score=34.33 Aligned_cols=61 Identities=15% Similarity=0.307 Sum_probs=32.1
Q ss_pred cceeeeecCCCeeecCcccCCCCCCC--hhh-hHHHHhhh-hchHHHHHHHHcCccCCCCCCccee
Q 009562 168 EVCEVECACGAQFCFSCLSEAHSPCS--CSM-WDLWAKKC-RDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 168 ~~~~v~C~C~~~fC~~C~~~~H~p~~--C~~-~~~w~~~~-~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
....+.|.||++||-. ...|....+ -.. ..+..+.. ..+...-+|+...--.||.|+++.+
T Consensus 67 ~~rv~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 67 QKRVIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred cccEEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 3346789999999975 333422111 000 00111100 1122234676665568999999887
No 98
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=72.54 E-value=2.4 Score=45.10 Aligned_cols=11 Identities=36% Similarity=1.123 Sum_probs=7.2
Q ss_pred ccccccccccc
Q 009562 60 MCDICMEEVAG 70 (532)
Q Consensus 60 ~C~IC~e~~~~ 70 (532)
.|.-|-.++..
T Consensus 276 iC~~C~K~V~g 286 (468)
T KOG1701|consen 276 ICAFCHKTVSG 286 (468)
T ss_pred hhhhcCCcccC
Confidence 67777776553
No 99
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=70.91 E-value=0.64 Score=46.92 Aligned_cols=35 Identities=31% Similarity=0.623 Sum_probs=26.7
Q ss_pred HHcCccCCCCCCcceeecCCCCeeEe-ccCceeecccccccC
Q 009562 214 ITVHTKPCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCGGATG 254 (532)
Q Consensus 214 i~~~tK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~~~ 254 (532)
+..++.+|--|-...+ |-+| .|||-|||-|...|-
T Consensus 235 i~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHH
Confidence 3445677777777665 5788 499999999999864
No 100
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=70.14 E-value=2.5 Score=42.73 Aligned_cols=43 Identities=26% Similarity=0.776 Sum_probs=33.2
Q ss_pred cccccccccccccCceec-CCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 59 VMCDICMEEVAGDKATKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
..|+.|-..+. ++... .|+|.||..|+..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhh--CcccCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 78999988754 55555 79999999999876654 3489998 664
No 101
>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=70.09 E-value=5.9 Score=26.45 Aligned_cols=28 Identities=25% Similarity=0.646 Sum_probs=16.3
Q ss_pred CccCCCCCCcceeecCCCCeeEec-cCce
Q 009562 217 HTKPCPKCHKPVEKNGGCNLVSCI-CGQA 244 (532)
Q Consensus 217 ~tK~CPkC~~~IEKn~GCnhMtC~-C~~~ 244 (532)
+.+-||+|+.+.+...+=--|.|. |++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 347888888888887776778884 7764
No 102
>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=69.93 E-value=1.5 Score=37.35 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=26.3
Q ss_pred cccccccccccccccCceecCCCCcccHHHHH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWT 88 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 88 (532)
+...|++|...+..+.++..||||.|...|.+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 45569999999876666667999999999975
No 103
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=69.78 E-value=2.3 Score=43.14 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=30.6
Q ss_pred ccccccccccccccC-ceecCCCCcccHHHHHHHHHhh
Q 009562 58 TVMCDICMEEVAGDK-ATKMDCGHCFCNDCWTEHFIVK 94 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yl~~~ 94 (532)
...|.||+--|...+ ++...|.|+|...|+..|+...
T Consensus 115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 467888888776655 5667999999999999999873
No 104
>cd07630 BAR_SNX_like The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of uncharacterized proteins with similarity to sorting nexins (SNXs), which are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=69.52 E-value=95 Score=30.05 Aligned_cols=63 Identities=13% Similarity=0.269 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 372 EIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 434 (532)
Q Consensus 372 ~~~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 434 (532)
..++..-|..|+.++..-|.+++.+..++..|..+.+.++|.-++.+...--.+.++.++.+.
T Consensus 131 ~~k~~~ae~~~~~a~~~fe~iS~~~k~EL~rF~~~Rv~~fk~~l~~~~E~~i~~ak~~~~~~~ 193 (198)
T cd07630 131 PQKKEQAEEAKKKAETEFEEISSLAKKELERFHRQRVLELQSALVCYAESQIKNAKEAAAVLT 193 (198)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567888888999999999999998887777777777887777777777777777766654
No 105
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=69.41 E-value=4.3 Score=29.48 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=19.7
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCceeec
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQAFCW 247 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~FCw 247 (532)
-.||+|+..++-..+=..++|. ||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 4689999888765443367884 8776643
No 106
>PHA03096 p28-like protein; Provisional
Probab=68.89 E-value=2.7 Score=42.96 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=29.0
Q ss_pred cccccccccccc----cCcee-c-CCCCcccHHHHHHHHHhhh
Q 009562 59 VMCDICMEEVAG----DKATK-M-DCGHCFCNDCWTEHFIVKI 95 (532)
Q Consensus 59 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~C~~~yl~~~i 95 (532)
..|+||++.+.. +..+. + .|.|.||..|++.+..+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~ 221 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL 221 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh
Confidence 689999998542 22333 3 8999999999999998865
No 107
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=68.57 E-value=2.3 Score=30.40 Aligned_cols=28 Identities=36% Similarity=0.799 Sum_probs=19.5
Q ss_pred CCCCCcceeecCCCCeeEeccCceeeccccccc
Q 009562 221 CPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 253 (532)
Q Consensus 221 CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~ 253 (532)
||-|...+. +-++=.|||.||..|+..+
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~ 28 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERL 28 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHH
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHH
Confidence 566666655 3366679999999999885
No 108
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=68.24 E-value=7.7 Score=40.00 Aligned_cols=53 Identities=21% Similarity=0.455 Sum_probs=37.5
Q ss_pred cccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHh
Q 009562 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLV 123 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll 123 (532)
..+-++||||++.+.. ..+..+=||..|.+|-.. ..-+||. |...++ .++.+.
T Consensus 45 ~~~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g--~~R~~a 97 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG--NIRCRA 97 (299)
T ss_pred chhhccCchhhccCcc-cceecCCCcEehhhhhhh-----------hcccCCc--cccccc--cHHHHH
Confidence 3456899999998752 334445589999999762 3468998 998887 445444
No 109
>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=67.41 E-value=1.1e+02 Score=30.19 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009562 378 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDL 437 (532)
Q Consensus 378 fe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l 437 (532)
-|..|++.+..-|.+++.+.+++..|....+.++|.-++.++..--++++..+.-+.+-|
T Consensus 156 AE~~~~~a~~~Fe~iS~~~k~El~rF~~~Rv~~fk~~lve~aE~~ik~Ak~~~~~l~~~~ 215 (219)
T cd07621 156 AEAAQQEACEKFESMSESAKQELLDFKTRRVAAFRKNLVELAELEIKHAKAQIQLLKNCL 215 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455778899999999999999988888888999999999999999999999998887655
No 110
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=67.41 E-value=1.6 Score=35.41 Aligned_cols=48 Identities=25% Similarity=0.576 Sum_probs=33.8
Q ss_pred ccccccccccc---------cCc-eec-CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 60 MCDICMEEVAG---------DKA-TKM-DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 60 ~C~IC~e~~~~---------~~~-~~l-~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
+|.||--.|+. ++. ..+ -|.|.|-.-|+.+++.+.-++| .||. |.+.+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~-----~CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG-----QCPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc-----cCCc--chhee
Confidence 67777766552 222 222 6899999999999999876655 4888 77654
No 111
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=65.70 E-value=2.4 Score=43.49 Aligned_cols=85 Identities=27% Similarity=0.654 Sum_probs=46.1
Q ss_pred CCcccHHHHHHHHHhhhccCCcccccccccccccccChHHHHHHhcCCChhHHHHHHHHH-HHHhhh----cccccccCC
Q 009562 79 GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFL-LESFIE----DNKMVKWCP 153 (532)
Q Consensus 79 gH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l-~~~~v~----~~~~~~~CP 153 (532)
|-.||..|-..+.. .|+.||. |...+ +++ +.+...|..+. ++.|.+ ...+...|-
T Consensus 275 ~Gy~CP~CkakvCs--------LP~eCpi--C~ltL-------Vss---~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf 334 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCS--------LPIECPI--CSLTL-------VSS---PHLARSYHHLFPLKPFVEIPETEYNGSRFCF 334 (378)
T ss_pred CceeCCcccCeeec--------CCccCCc--cceeE-------ecc---hHHHHHHHhhcCCcchhhccccccCCCccee
Confidence 34567777554433 5788887 77543 112 44444454332 222322 222344564
Q ss_pred CCCCCCceEEeccccceeeee-cCCCeeecCcccCCCC
Q 009562 154 STPHCGNAIRVEEVEVCEVEC-ACGAQFCFSCLSEAHS 190 (532)
Q Consensus 154 ~~p~C~~~i~~~~~~~~~v~C-~C~~~fC~~C~~~~H~ 190 (532)
.|+. +........| .|...||..|..-.|.
T Consensus 335 ---~C~~----~~~~~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 335 ---ACQG----ELLSSGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred ---eecc----ccCCCCcEEchhccceeeccchHHHHh
Confidence 4521 1223345789 5999999999876664
No 112
>PLN03086 PRLI-interacting factor K; Provisional
Probab=65.61 E-value=11 Score=42.21 Aligned_cols=57 Identities=26% Similarity=0.572 Sum_probs=35.7
Q ss_pred ccccccccccccccChHHHHHHhcCCChhHHHHHHHHHHHHhhhcccccccCCCCCCCCceEEeccccceeeeec-CCCe
Q 009562 101 KRIRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 179 (532)
Q Consensus 101 ~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 179 (532)
..+.||. |+..++...+...+. .-..+.+-|| ..+|+..+....-. .-..|+ |+..
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~-------------------~C~r~~V~Cp-~~~Cg~v~~r~el~-~H~~C~~Cgk~ 462 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEA-------------------YCSRHNVVCP-HDGCGIVLRVEEAK-NHVHCEKCGQA 462 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHh-------------------hCCCcceeCC-cccccceeeccccc-cCccCCCCCCc
Confidence 3468998 998887666553332 1223456799 46799988755522 224775 8776
Q ss_pred e
Q 009562 180 F 180 (532)
Q Consensus 180 f 180 (532)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 5
No 113
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.46 E-value=5.9 Score=38.64 Aligned_cols=55 Identities=20% Similarity=0.409 Sum_probs=42.2
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.-.|..|-.++...+.+.+.|-|.|.-.|+.+.-..--....-.-..||. |...|
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 34799999999888999999999999999998765433322224578998 88654
No 114
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=61.17 E-value=1.3e+02 Score=29.64 Aligned_cols=60 Identities=18% Similarity=0.219 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009562 378 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDL 437 (532)
Q Consensus 378 fe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l 437 (532)
-|..|++.+..-|++|+.+..++..|...-+..+|.-++.+...--++++.-+.-+.+-|
T Consensus 155 aE~~~~~a~~~Fe~IS~~aK~El~rF~~~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~~~~~ 214 (218)
T cd07662 155 AETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQLLQSCL 214 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 377888999999999999998877776666777787777777777777777666665433
No 115
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=61.04 E-value=3.9 Score=32.18 Aligned_cols=21 Identities=29% Similarity=0.838 Sum_probs=9.4
Q ss_pred cCCCCCCcceee---cCCCCeeEe
Q 009562 219 KPCPKCHKPVEK---NGGCNLVSC 239 (532)
Q Consensus 219 K~CPkC~~~IEK---n~GCnhMtC 239 (532)
-+|++|...+.. .+||.|++|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fC 31 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFC 31 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-
T ss_pred cCCcHHHHHhcCCceeccCccHHH
Confidence 589999988765 377877766
No 116
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.41 E-value=4.4 Score=46.86 Aligned_cols=37 Identities=30% Similarity=0.665 Sum_probs=30.9
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHh
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIV 93 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~ 93 (532)
..-.|.+|.-.+-...++..+|||.|..+|+..+...
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~ 852 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLS 852 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHc
Confidence 4568999999877666667799999999999988765
No 117
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=60.04 E-value=8.8 Score=26.53 Aligned_cols=28 Identities=29% Similarity=0.797 Sum_probs=20.6
Q ss_pred ccCCCCCCCCceEEecc----ccceeeeec-CCCee
Q 009562 150 KWCPSTPHCGNAIRVEE----VEVCEVECA-CGAQF 180 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-C~~~f 180 (532)
.-|| .|+..+.+++ .....+.|+ |++.|
T Consensus 3 i~Cp---~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP---NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC---CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 3587 7999888776 344578995 98876
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.62 E-value=9.1 Score=26.57 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEEeccc----cceeeeec-CCCee
Q 009562 150 KWCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 180 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 180 (532)
.-|| .|+..+.++++ ....|.|+ |++.|
T Consensus 3 i~CP---~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP---NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC---CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4688 79999887763 34578996 98876
No 119
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=59.38 E-value=6.5 Score=27.03 Aligned_cols=27 Identities=37% Similarity=0.943 Sum_probs=17.0
Q ss_pred ccCCCCCCCCceEEeccccceeeeec-CCCe
Q 009562 150 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 179 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 179 (532)
++|| .|++.+....+....+.|. |++.
T Consensus 2 ~FCp---~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP---ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BET---TTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCC---CCCccceEcCCCccCcCCCCCCCc
Confidence 5788 7999998766443333673 7665
No 120
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=58.33 E-value=8.8 Score=25.57 Aligned_cols=25 Identities=28% Similarity=0.760 Sum_probs=12.4
Q ss_pred CCCCCCcceeecCCCCeeEec-cCcee
Q 009562 220 PCPKCHKPVEKNGGCNLVSCI-CGQAF 245 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC~-C~~~F 245 (532)
.||+|+....-.+|.+ |.|. |+++|
T Consensus 4 ~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCcceeccCCE-EeCCcccccC
Confidence 6999998887777754 6784 88775
No 121
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.79 E-value=9.7 Score=38.51 Aligned_cols=54 Identities=24% Similarity=0.535 Sum_probs=40.0
Q ss_pred ccccccccccccccccCceecC--CCCcccHHHHHHHHHhhhccCCcccccccc-ccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKMD--CGHCFCNDCWTEHFIVKINEGQSKRIRCMA-HKCNA 112 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~-~~C~~ 112 (532)
.....|.+|-|-+....++..+ =.|.||.-|-++.|+.+-..|. +.||. .+|..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sge---vYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGE---VYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCc---eeCCCCCcCcc
Confidence 3468999999997744444432 2699999999999998765554 88986 45764
No 122
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=57.30 E-value=7.8 Score=32.96 Aligned_cols=28 Identities=36% Similarity=0.765 Sum_probs=21.1
Q ss_pred CCCCCCcce--eecCCCCeeEec-cCceeec
Q 009562 220 PCPKCHKPV--EKNGGCNLVSCI-CGQAFCW 247 (532)
Q Consensus 220 ~CPkC~~~I--EKn~GCnhMtC~-C~~~FCw 247 (532)
-||.|+..+ ++.+-||...|+ |.+.|=-
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 699999754 455559999996 9987643
No 123
>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=57.14 E-value=8.9 Score=26.16 Aligned_cols=26 Identities=19% Similarity=0.452 Sum_probs=22.8
Q ss_pred CCCCCCc-ceeecCCCCeeEec-cCceeecccccc
Q 009562 220 PCPKCHK-PVEKNGGCNLVSCI-CGQAFCWLCGGA 252 (532)
Q Consensus 220 ~CPkC~~-~IEKn~GCnhMtC~-C~~~FCw~C~~~ 252 (532)
.||.|.. ++. ++|. |+...|..|...
T Consensus 2 ~C~~H~~~~~~-------~fC~~~~~~iC~~C~~~ 29 (39)
T cd00021 2 LCDEHGEEPLS-------LFCETDRALLCVDCDLS 29 (39)
T ss_pred CCCccCCcceE-------EEeCccChhhhhhcChh
Confidence 5899987 888 9995 999999999865
No 124
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=57.06 E-value=4.5 Score=42.56 Aligned_cols=49 Identities=22% Similarity=0.631 Sum_probs=37.9
Q ss_pred cccccccccccccc--ccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 56 SSTVMCDICMEEVA--GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 56 ~~~~~C~IC~e~~~--~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
+....|..|.+.+. .+....++|.|.|...|+.+|+.. ++ +-.||. |+.
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HHH
Confidence 34678999999854 345667899999999999999953 33 368998 773
No 125
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=56.95 E-value=4 Score=31.07 Aligned_cols=45 Identities=27% Similarity=0.645 Sum_probs=30.9
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
...|-.|... ....+.++|||..|..||-.- .---||. |...+..
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEF 51 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChh----------hccCCCC--CCCcccC
Confidence 4556677655 235667899999999998642 1236888 8876643
No 126
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=56.22 E-value=6.9 Score=45.58 Aligned_cols=52 Identities=23% Similarity=0.464 Sum_probs=37.5
Q ss_pred ccccccccccccccccC---cee--cCCCCcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 56 SSTVMCDICMEEVAGDK---ATK--MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~---~~~--l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
+...+|+||+..+..-+ |.. -.|.|.|...|+-.|+... ..-+||. |...++
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 34568999999865221 221 2689999999999999873 2358998 876554
No 127
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.08 E-value=2.7 Score=39.64 Aligned_cols=30 Identities=37% Similarity=0.978 Sum_probs=22.1
Q ss_pred ecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 174 CACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 174 C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
=.||+.||..|-+.+ ..++..||-|++-|.
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 359999999986531 234589999998665
No 128
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=55.78 E-value=6.4 Score=45.78 Aligned_cols=26 Identities=38% Similarity=1.064 Sum_probs=22.5
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCceee
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQAFC 246 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~FC 246 (532)
..||.|+..+...+||. +|+ ||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999995 996 998766
No 129
>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=54.53 E-value=21 Score=24.33 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=24.3
Q ss_pred ccCCHHHHHHHHHHcCCChHHHHHHHH
Q 009562 4 LSLREHHARTLLIHYRWDVEKLLAVLV 30 (532)
Q Consensus 4 l~i~~~~a~~LL~~~~W~~~~l~~~~~ 30 (532)
+|.+.+.|+.-|+.++||+++.++.++
T Consensus 11 mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 11 MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 588999999999999999999988765
No 130
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=54.25 E-value=11 Score=30.13 Aligned_cols=32 Identities=41% Similarity=0.970 Sum_probs=20.9
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCc-----eeeccccccc
Q 009562 220 PCPKCHKPVEKNGGCNLVSC-ICGQ-----AFCWLCGGAT 253 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC-~C~~-----~FCw~C~~~~ 253 (532)
.||.|+.+++.++ .+.+| .|+. .+|-.|+.+.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 6999999999888 68999 4885 4688888773
No 131
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.73 E-value=10 Score=43.87 Aligned_cols=35 Identities=29% Similarity=0.790 Sum_probs=29.5
Q ss_pred ccCCCCCCcceeecCCCCeeEec-cCce-----eecccccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCI-CGQA-----FCWLCGGA 252 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~-C~~~-----FCw~C~~~ 252 (532)
+-.||+|..++.-...=|.|.|. ||++ .|.-|++.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 35899999998866666999995 9987 89999987
No 132
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.25 E-value=12 Score=32.89 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=24.8
Q ss_pred ccCCCCCCCCceEEecc-------ccceeeeec-CCCeeecCcccCCCC
Q 009562 150 KWCPSTPHCGNAIRVEE-------VEVCEVECA-CGAQFCFSCLSEAHS 190 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~-------~~~~~v~C~-C~~~fC~~C~~~~H~ 190 (532)
+.|- +|...+.... .......|+ |+..||..|..-+|.
T Consensus 56 ~~C~---~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF---GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc---CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4575 6776554221 112245795 999999999887775
No 133
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=53.07 E-value=9.9 Score=34.24 Aligned_cols=24 Identities=46% Similarity=1.108 Sum_probs=18.4
Q ss_pred ccCCCCCCcceeecCCCCeeEeccCceeecccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCG 250 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~ 250 (532)
.+.||.|+.|+-+ +-|.-||-+|+
T Consensus 28 ~~hCp~Cg~PLF~---------KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFR---------KDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCccee---------eCCeEECCCCC
Confidence 3789999999964 34567777777
No 134
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=53.05 E-value=12 Score=38.17 Aligned_cols=47 Identities=30% Similarity=0.619 Sum_probs=36.6
Q ss_pred ccccccccccccccc--cCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 56 SSTVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
...+.||||.+.+.. ..+..++|||..-..|+..++.. . +.||. |..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 345679999998532 34556799999999999998764 2 79998 887
No 135
>PRK04023 DNA polymerase II large subunit; Validated
Probab=52.76 E-value=10 Score=44.77 Aligned_cols=33 Identities=30% Similarity=0.644 Sum_probs=20.5
Q ss_pred cccccccCCCCCCCCceEEeccccceeeeec-CCC-----eeecCcccC
Q 009562 145 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGA-----QFCFSCLSE 187 (532)
Q Consensus 145 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~-----~fC~~C~~~ 187 (532)
.....+.|| .|+... ....|+ ||. .||..|+..
T Consensus 622 VEVg~RfCp---sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 622 VEIGRRKCP---SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ecccCccCC---CCCCcC-------CcccCCCCCCCCCcceeCccccCc
Confidence 334567887 687653 235776 875 377777554
No 136
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.35 E-value=14 Score=36.62 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=18.5
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCceeecccc
Q 009562 220 PCPKCHKPVEKNGGCNLVSC-ICGQAFCWLCG 250 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~ 250 (532)
.|+.+... .+++| .|+...|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEecccccccCCCCC
Confidence 45555554 55999 59999999998
No 137
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.18 E-value=6.2 Score=40.04 Aligned_cols=29 Identities=31% Similarity=0.881 Sum_probs=23.9
Q ss_pred ccccccccccccccCceecCCCCc-ccHHHHH
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHC-FCNDCWT 88 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~ 88 (532)
...|.||+|. +-+.+.|+|||. -|..|=+
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhcc
Confidence 6789999998 448899999997 6888843
No 138
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.72 E-value=10 Score=43.23 Aligned_cols=13 Identities=23% Similarity=0.695 Sum_probs=10.1
Q ss_pred CccCCCCCCccee
Q 009562 217 HTKPCPKCHKPVE 229 (532)
Q Consensus 217 ~tK~CPkC~~~IE 229 (532)
+.+.||+|+..+.
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 3488999998876
No 139
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=51.55 E-value=11 Score=28.10 Aligned_cols=26 Identities=27% Similarity=0.604 Sum_probs=14.8
Q ss_pred ccCCCCCCcceeecCCCCeeEe-ccCc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSC-ICGQ 243 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC-~C~~ 243 (532)
-+.||+|+--+--..-=+...| +||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 3789999953332222225677 6764
No 140
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=51.03 E-value=3.9 Score=42.06 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=22.0
Q ss_pred ccCCCCCCcceee-cCCCCeeEe-ccCcee
Q 009562 218 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 245 (532)
Q Consensus 218 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 245 (532)
|.+||+|+..|-+ .-.=|.+.| +|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 6899999998864 445567899 599988
No 141
>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=50.89 E-value=13 Score=29.11 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=19.0
Q ss_pred CccCCCCCCcceeecCCCCeeEec-cCce
Q 009562 217 HTKPCPKCHKPVEKNGGCNLVSCI-CGQA 244 (532)
Q Consensus 217 ~tK~CPkC~~~IEKn~GCnhMtC~-C~~~ 244 (532)
.++.||.|+...+++..=..++|. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 468999999999973333356663 6554
No 142
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.76 E-value=8 Score=40.40 Aligned_cols=44 Identities=25% Similarity=0.609 Sum_probs=30.6
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
+..-.|.||.++.. +..-++|||.-| |..-+- ..+.||. |...+
T Consensus 303 ~~p~lcVVcl~e~~--~~~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPK--SAVFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCCceEEecCCcc--ceeeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 45678999999854 677789999976 544332 1256998 87544
No 143
>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=50.66 E-value=17 Score=25.00 Aligned_cols=27 Identities=33% Similarity=0.870 Sum_probs=18.8
Q ss_pred cCCCCCCCCceEEeccc----cceeeeec-CCCee
Q 009562 151 WCPSTPHCGNAIRVEEV----EVCEVECA-CGAQF 180 (532)
Q Consensus 151 ~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 180 (532)
-|| .|+..+.+.++ ....+.|+ |++.|
T Consensus 4 ~CP---~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCP---NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECC---CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 577 79998887652 23368885 88765
No 144
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.25 E-value=11 Score=37.46 Aligned_cols=37 Identities=14% Similarity=0.221 Sum_probs=31.6
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhcc
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINE 97 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~ 97 (532)
-.|+.|+..+. +++..+=||.||+.||-+||..+-++
T Consensus 44 dcCsLtLqPc~--dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 44 DCCSLTLQPCR--DPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ceeeeeccccc--CCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 36889998866 88888999999999999999886543
No 145
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=49.93 E-value=5.2 Score=38.48 Aligned_cols=31 Identities=32% Similarity=0.774 Sum_probs=23.4
Q ss_pred ccCCCCCCcceeecCCCCeeEeccCceeeccccccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 253 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~ 253 (532)
.-.||-|.-.+.. . +.=.|||-|||.|...|
T Consensus 18 ~~~CpICld~~~d--P---VvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 18 DFDCNICLDQVRD--P---VVTLCGHLFCWPCIHKW 48 (193)
T ss_pred ccCCccCCCcCCC--c---EEcCCCchhHHHHHHHH
Confidence 3589999887641 1 33369999999999887
No 146
>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=49.83 E-value=18 Score=24.86 Aligned_cols=24 Identities=21% Similarity=0.227 Sum_probs=21.0
Q ss_pred cCCHHHHHHHHHHcCCChHHHHHH
Q 009562 5 SLREHHARTLLIHYRWDVEKLLAV 28 (532)
Q Consensus 5 ~i~~~~a~~LL~~~~W~~~~l~~~ 28 (532)
|.+.+.|+.-|+..+||++..++.
T Consensus 13 Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 13 GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 899999999999999999998764
No 147
>cd07663 BAR_SNX5 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5. 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. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It
Probab=49.56 E-value=2.7e+02 Score=27.46 Aligned_cols=60 Identities=18% Similarity=0.235 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009562 378 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDL 437 (532)
Q Consensus 378 fe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l 437 (532)
-|..|.+.+..-|.+|+.+.+++..|....+.++|.-++.+....-++++.-+..+.+-|
T Consensus 155 aE~~~~ea~~~Fe~IS~~~k~El~rF~~~Rv~~Fk~~lve~~E~~ik~ak~~~~~~~~~~ 214 (218)
T cd07663 155 AEAHQQECCQKFEKLSESAKQELISFKRRRVAAFRKNLIEMTELEIKHAKNNVSLLQSCI 214 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566777889999999999998887777777788888888887777777777776665443
No 148
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.46 E-value=16 Score=34.40 Aligned_cols=57 Identities=25% Similarity=0.472 Sum_probs=38.5
Q ss_pred ccccccccccc-ccccC----ceecCCCCcccHHHHHHHHHhhhccCCcccc---cccccccccccC
Q 009562 57 STVMCDICMEE-VAGDK----ATKMDCGHCFCNDCWTEHFIVKINEGQSKRI---RCMAHKCNAICD 115 (532)
Q Consensus 57 ~~~~C~IC~e~-~~~~~----~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i---~CP~~~C~~~~~ 115 (532)
....|.||+-- ++.+- .-...||..|..-|+..|+..-+...+++.| .||- |..++.
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 44567777753 22111 1235799999999999999987777666555 6877 776553
No 149
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=49.46 E-value=9.3 Score=33.36 Aligned_cols=25 Identities=32% Similarity=0.874 Sum_probs=16.6
Q ss_pred cCCCCCCccee-ecCCCCeeEe-ccCcee
Q 009562 219 KPCPKCHKPVE-KNGGCNLVSC-ICGQAF 245 (532)
Q Consensus 219 K~CPkC~~~IE-Kn~GCnhMtC-~C~~~F 245 (532)
+.||+|++..- .|- +-++| +||..|
T Consensus 10 R~Cp~CG~kFYDLnk--~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK--DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC--CCccCCCCCCcc
Confidence 68999997665 233 66777 466654
No 150
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=49.36 E-value=4.8 Score=45.84 Aligned_cols=30 Identities=30% Similarity=0.878 Sum_probs=21.5
Q ss_pred cCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 175 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 175 ~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
.|+|.||+.|-... +....+.||+|+.+.-
T Consensus 660 kC~H~FC~~Cvq~r-------------------------~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 660 KCGHVFCEECVQTR-------------------------YETRQRKCPKCNAAFG 689 (698)
T ss_pred hcchHHHHHHHHHH-------------------------HHHhcCCCCCCCCCCC
Confidence 49999999996531 1123389999998764
No 151
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=48.30 E-value=25 Score=23.85 Aligned_cols=26 Identities=19% Similarity=0.163 Sum_probs=23.0
Q ss_pred ccCCHHHHHHHHHHcCCChHHHHHHH
Q 009562 4 LSLREHHARTLLIHYRWDVEKLLAVL 29 (532)
Q Consensus 4 l~i~~~~a~~LL~~~~W~~~~l~~~~ 29 (532)
+|.+.+.|+.-|+..+||+++.++-+
T Consensus 11 mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 11 MGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 58999999999999999999887654
No 152
>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=48.07 E-value=15 Score=26.31 Aligned_cols=22 Identities=36% Similarity=1.200 Sum_probs=15.9
Q ss_pred cCCCCCCcceee-cCCCCeeEec-cC
Q 009562 219 KPCPKCHKPVEK-NGGCNLVSCI-CG 242 (532)
Q Consensus 219 K~CPkC~~~IEK-n~GCnhMtC~-C~ 242 (532)
..||.|+.|+-+ .+| .++|. |+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 689999999987 444 46663 53
No 153
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=47.79 E-value=2.7e+02 Score=26.95 Aligned_cols=96 Identities=16% Similarity=0.290 Sum_probs=47.4
Q ss_pred cccchhHHHHHHHHHHHHHHhhhccccceeeccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCC
Q 009562 325 RLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYP 404 (532)
Q Consensus 325 ~~~~~~~l~~a~~~l~~~R~vL~~Sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~ 404 (532)
+++++.....+++.+++.|....+.|... .+....+...++..-+......+...+.+.+++..+.
T Consensus 99 ~LkEy~~ya~slk~vlk~r~~~q~~~e~~--------------~~~L~~k~~~l~~~ve~a~~~~e~f~~~~~~E~~rF~ 164 (201)
T cd07622 99 QLKEYLFFADSLRAVCKKHELLQYDLEKA--------------EDALANKKQQGEEAVKEAKDELNEFVKKALEDVERFK 164 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677777888888888777776644332 1111222222222222222223333333333444444
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 405 DDKVMEIRMQVINLSVITDTLCKKMYECIE 434 (532)
Q Consensus 405 ~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 434 (532)
..+..++|.-+.++...=-.+++++++.-+
T Consensus 165 ~~K~~dlk~~l~~~A~~qi~~~~~~~~~W~ 194 (201)
T cd07622 165 KQKVRDLKEILISYAKLQIKLAKKGLQTWT 194 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555666666555555555555554443
No 154
>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=47.68 E-value=16 Score=40.50 Aligned_cols=34 Identities=26% Similarity=0.662 Sum_probs=23.8
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCce-----eecccccc
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQA-----FCWLCGGA 252 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~-----FCw~C~~~ 252 (532)
-.||+|..++.--..=|.+.|. ||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4788888877643334478884 8866 68888765
No 155
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=47.45 E-value=3.1e+02 Score=27.51 Aligned_cols=99 Identities=11% Similarity=0.224 Sum_probs=60.0
Q ss_pred cccchhHHHHHHHHHHHHHHhhhccccceeeccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCC
Q 009562 325 RLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYP 404 (532)
Q Consensus 325 ~~~~~~~l~~a~~~l~~~R~vL~~Sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~ 404 (532)
.++|+-.+..|++.++.-|-.+...|... .+.-...+.. +.-.+...+.+|..++..+..|..++..+.
T Consensus 140 ~Lkeyv~y~~slK~vlk~R~~~Q~~le~k----------~e~l~k~~~d-r~~~~~ev~~~e~kve~a~~~~k~e~~Rf~ 208 (243)
T cd07666 140 VIHEYVLYSETLMGVIKRRDQIQAELDSK----------VEALANKKAD-RDLLKEEIEKLEDKVECANNALKADWERWK 208 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666677888888888776554433222 0000000111 134444555666777777777777776666
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 405 DDKVMEIRMQVINLSVITDTLCKKMYECIE 434 (532)
Q Consensus 405 ~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 434 (532)
..+..++|.-+++....--.++++++..-|
T Consensus 209 ~~k~~D~k~~~~~yae~~i~~~~~~~~~We 238 (243)
T cd07666 209 QNMQTDLRSAFTDMAENNISYYEECLATWE 238 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677777777777777777777777776665
No 156
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.02 E-value=4.6e+02 Score=29.43 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHH
Q 009562 378 FEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVI 416 (532)
Q Consensus 378 fe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~ 416 (532)
..+.|+.|++...+|.......+....+++ .++|++++
T Consensus 628 a~e~qe~L~~~~~~L~~~~~~~lp~l~~AE-rdFk~Elq 665 (741)
T KOG4460|consen 628 AKEKQEDLMNRMKKLLHSFHSELPVLSDAE-RDFKKELQ 665 (741)
T ss_pred HHHhHHHHHHHHHHHHhcccccCCcchhHH-HHHHHHHH
Confidence 344567777777777776666655554443 34555553
No 157
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=45.53 E-value=16 Score=26.83 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=23.0
Q ss_pred cccccccccccCceecCCC--C---cccHHHHHHHHHh
Q 009562 61 CDICMEEVAGDKATKMDCG--H---CFCNDCWTEHFIV 93 (532)
Q Consensus 61 C~IC~e~~~~~~~~~l~Cg--H---~fC~~C~~~yl~~ 93 (532)
|-||+++...+++...+|+ - ....+|+..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 7799998665555556665 2 5788999999987
No 158
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.00 E-value=18 Score=27.53 Aligned_cols=32 Identities=28% Similarity=0.858 Sum_probs=25.7
Q ss_pred cccccccccccc-ccCceec-CCCCcccHHHHHH
Q 009562 58 TVMCDICMEEVA-GDKATKM-DCGHCFCNDCWTE 89 (532)
Q Consensus 58 ~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~C~~~ 89 (532)
...|++|-+.|. .++.+.. .||-.|.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999985 4566665 8999999999965
No 159
>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=44.52 E-value=37 Score=29.86 Aligned_cols=42 Identities=24% Similarity=0.646 Sum_probs=29.1
Q ss_pred CccCCCCCCcceeecCCCCeeEec-cCceeecccccccCCCCCc
Q 009562 217 HTKPCPKCHKPVEKNGGCNLVSCI-CGQAFCWLCGGATGRDHTW 259 (532)
Q Consensus 217 ~tK~CPkC~~~IEKn~GCnhMtC~-C~~~FCw~C~~~~~~~H~w 259 (532)
+.+.|..|+.+.-.-.+.. ..|. |++.+|-.|+........|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~~~~~~~W 95 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVYSKKEPIW 95 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEETSSSCCE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCcCCCCCCE
Confidence 5689999999876544444 8895 9999999999873333334
No 160
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.11 E-value=17 Score=44.13 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 009562 380 DQQQQLEANVEKLSKF 395 (532)
Q Consensus 380 ~~q~~lE~~~E~L~~~ 395 (532)
+.=..+--.+|+|.++
T Consensus 797 frp~Eigvs~eklreL 812 (1337)
T PRK14714 797 FRPREIGVSVEKLREL 812 (1337)
T ss_pred ccHHHcCCCHHHHHHc
Confidence 3344566677788776
No 161
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=44.08 E-value=18 Score=32.70 Aligned_cols=53 Identities=25% Similarity=0.489 Sum_probs=39.2
Q ss_pred cccccccccccccccccCceec--CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 55 LSSTVMCDICMEEVAGDKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.+.-.+|.||-|....+.+... -||=..|.-|....|...- ....||. |+..+
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 3457899999998553332222 4999999999999998753 3578999 88765
No 162
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=43.77 E-value=5.4 Score=40.97 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=15.5
Q ss_pred ccCCCCCCcceee-cCCCCeeEe-ccCcee
Q 009562 218 TKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 245 (532)
Q Consensus 218 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 245 (532)
|.+||+|+..|-+ .-.=|...| .|+++|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3567777766653 233445566 366654
No 163
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=43.76 E-value=5.1 Score=29.80 Aligned_cols=34 Identities=29% Similarity=0.773 Sum_probs=28.3
Q ss_pred cccccccccccccccCceec-CCCCcccHHHHHHH
Q 009562 57 STVMCDICMEEVAGDKATKM-DCGHCFCNDCWTEH 90 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~y 90 (532)
..++|..|-+.++..+.... -||---|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 57899999999887666554 79999999999873
No 164
>PF14369 zf-RING_3: zinc-finger
Probab=43.41 E-value=20 Score=24.67 Aligned_cols=28 Identities=29% Similarity=0.883 Sum_probs=18.9
Q ss_pred ccCCCCCCCCceEEeccccceeeeec-CCCee
Q 009562 150 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQF 180 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~f 180 (532)
.||- .|...+.........+.|| |+..|
T Consensus 3 ywCh---~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH---QCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCc---cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 4897 7999998754333345686 77655
No 165
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.41 E-value=21 Score=24.44 Aligned_cols=25 Identities=36% Similarity=0.891 Sum_probs=11.6
Q ss_pred cCCCCCCcceeec----CCCCeeEec-cCc
Q 009562 219 KPCPKCHKPVEKN----GGCNLVSCI-CGQ 243 (532)
Q Consensus 219 K~CPkC~~~IEKn----~GCnhMtC~-C~~ 243 (532)
|-||.|+.+++.. ++=..+.|. ||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4688888888852 445556773 664
No 166
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=43.23 E-value=2.1e+02 Score=30.82 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009562 372 EIKQHLFEDQQQQLEANVEKLSKFLE 397 (532)
Q Consensus 372 ~~~~~lfe~~q~~lE~~~E~L~~~le 397 (532)
...++.||...+.-...++.|.+.||
T Consensus 47 ~rIkq~FekkNqksa~~i~~lqkkL~ 72 (395)
T PF10267_consen 47 ARIKQVFEKKNQKSAQTIAQLQKKLE 72 (395)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 45567777777777777777777766
No 167
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=43.20 E-value=16 Score=44.27 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=5.2
Q ss_pred cCCCCCCcce
Q 009562 219 KPCPKCHKPV 228 (532)
Q Consensus 219 K~CPkC~~~I 228 (532)
..||+|+..+
T Consensus 668 rkCPkCG~~t 677 (1337)
T PRK14714 668 RRCPSCGTET 677 (1337)
T ss_pred EECCCCCCcc
Confidence 4555555544
No 168
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=43.18 E-value=8.3 Score=39.43 Aligned_cols=53 Identities=26% Similarity=0.627 Sum_probs=37.5
Q ss_pred ccccccCCCCCCCCceEEeccccceeeeecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCC
Q 009562 146 NKMVKWCPSTPHCGNAIRVEEVEVCEVECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCH 225 (532)
Q Consensus 146 ~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~ 225 (532)
+..+-+|- .|+..|.+=+.- =+|.+.||..|... |. . |.||.|.
T Consensus 87 ~p~VHfCd---~Cd~PI~IYGRm-----IPCkHvFCl~CAr~-~~------------------d---------K~Cp~C~ 130 (389)
T KOG2932|consen 87 GPRVHFCD---RCDFPIAIYGRM-----IPCKHVFCLECARS-DS------------------D---------KICPLCD 130 (389)
T ss_pred CcceEeec---ccCCcceeeecc-----cccchhhhhhhhhc-Cc------------------c---------ccCcCcc
Confidence 34566776 788877643221 16999999999753 21 1 8999999
Q ss_pred cceeecCCC
Q 009562 226 KPVEKNGGC 234 (532)
Q Consensus 226 ~~IEKn~GC 234 (532)
-.|+|.+-|
T Consensus 131 d~VqrIeq~ 139 (389)
T KOG2932|consen 131 DRVQRIEQI 139 (389)
T ss_pred cHHHHHHHh
Confidence 999987765
No 169
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.11 E-value=19 Score=35.97 Aligned_cols=55 Identities=15% Similarity=0.312 Sum_probs=38.8
Q ss_pred cccccccccccccccCc--eecCCC-----CcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 57 STVMCDICMEEVAGDKA--TKMDCG-----HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~--~~l~Cg-----H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
..-.|=|||.+-..+.. ..-||. |-....|+..|+..+-......++.||+ |...
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 45689999987432221 122664 5689999999999887644457899999 8863
No 170
>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=43.02 E-value=16 Score=31.28 Aligned_cols=23 Identities=30% Similarity=0.781 Sum_probs=17.1
Q ss_pred CCCCCCcceeecCCCCeeEec-cCce
Q 009562 220 PCPKCHKPVEKNGGCNLVSCI-CGQA 244 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC~-C~~~ 244 (532)
.||+|+.++...+ +.+.|+ |++.
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCc
Confidence 6999999887654 367784 7765
No 171
>PF12773 DZR: Double zinc ribbon
Probab=42.96 E-value=10 Score=27.82 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=6.9
Q ss_pred cCCCCCCccee
Q 009562 219 KPCPKCHKPVE 229 (532)
Q Consensus 219 K~CPkC~~~IE 229 (532)
+.||+|+..+.
T Consensus 30 ~~C~~Cg~~~~ 40 (50)
T PF12773_consen 30 KICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCCc
Confidence 56666666654
No 172
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=42.77 E-value=9.9 Score=32.49 Aligned_cols=32 Identities=19% Similarity=0.494 Sum_probs=24.7
Q ss_pred cccccccccccccccccCceecCCCCcccHHH
Q 009562 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 86 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 86 (532)
....|+|.-||-....+....-.=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 46789999999886655555545689999998
No 173
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.41 E-value=20 Score=41.27 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=22.1
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCce----eecccccc
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQA----FCWLCGGA 252 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~----FCw~C~~~ 252 (532)
-.||+|..++.-..+=+.+.|. ||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4688888777754444568884 8753 46667654
No 174
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=42.11 E-value=7.7 Score=44.02 Aligned_cols=53 Identities=25% Similarity=0.580 Sum_probs=39.6
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHH
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAV 118 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~ 118 (532)
...+|+||+..+- +++.+.|.|.||..||..-+...-. ...||. |+..++...
T Consensus 20 k~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~s 72 (684)
T KOG4362|consen 20 KILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKRS 72 (684)
T ss_pred hhccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhhh
Confidence 3568999999865 6678899999999999987765322 467887 775554433
No 175
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.76 E-value=22 Score=29.65 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=21.7
Q ss_pred ccCCCCCCcceeecCCCCeeEe-ccCcee
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSC-ICGQAF 245 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 245 (532)
--.||.|+...-|..+=---.| +||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3689999999888777666777 477766
No 176
>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=41.61 E-value=6.4 Score=40.32 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=20.5
Q ss_pred ccCCCCCCcceeec-CCCCeeEe-ccCcee
Q 009562 218 TKPCPKCHKPVEKN-GGCNLVSC-ICGQAF 245 (532)
Q Consensus 218 tK~CPkC~~~IEKn-~GCnhMtC-~C~~~F 245 (532)
|..||+|+..|-+. -.=|.+.| .|+++|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 68899999888753 34566788 488875
No 177
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.27 E-value=17 Score=42.08 Aligned_cols=40 Identities=20% Similarity=0.578 Sum_probs=30.4
Q ss_pred cccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
-.|..|--++.. +++...|||.|...|+. ++. -.||. |..
T Consensus 841 skCs~C~~~Ldl-P~VhF~CgHsyHqhC~e--------~~~---~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDL-PFVHFLCGHSYHQHCLE--------DKE---DKCPK--CLP 880 (933)
T ss_pred eeecccCCcccc-ceeeeecccHHHHHhhc--------cCc---ccCCc--cch
Confidence 479999877652 45667999999999998 332 68987 875
No 178
>KOG4759 consensus Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=41.23 E-value=1.9e+02 Score=29.16 Aligned_cols=66 Identities=18% Similarity=0.183 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 009562 374 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLG 439 (532)
Q Consensus 374 ~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~ 439 (532)
...+|+..-++|-+--.+..+.+.......+++++.++..++.++.+...+....|++.-|.+|++
T Consensus 197 ~~~~~ee~K~slr~ir~~~~kk~~k~~~~~~~D~vkkae~~l~~l~k~~v~~ld~llkskeKellk 262 (263)
T KOG4759|consen 197 LKRYFEEYKQSLRKIRTKSIKKSKKNKKSLSEDEVKKAEAELQKLAKDAVNKLDDLLKSKEKELLK 262 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345566666666555555555555544457889999999999999999999999999999999874
No 179
>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=40.55 E-value=23 Score=26.47 Aligned_cols=11 Identities=45% Similarity=0.942 Sum_probs=8.8
Q ss_pred cCCCCCCccee
Q 009562 219 KPCPKCHKPVE 229 (532)
Q Consensus 219 K~CPkC~~~IE 229 (532)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 79999997555
No 180
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=40.19 E-value=26 Score=25.20 Aligned_cols=41 Identities=24% Similarity=0.601 Sum_probs=19.9
Q ss_pred cccccccccccCce-ecCCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 61 CDICMEEVAGDKAT-KMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 61 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
|.+|-+.+.....= ..+|+=.+...|+..||...- ..+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 66787765422111 125888999999999998732 127886
No 181
>PHA02929 N1R/p28-like protein; Provisional
Probab=39.57 E-value=8.2 Score=38.48 Aligned_cols=32 Identities=25% Similarity=0.753 Sum_probs=23.0
Q ss_pred eeecCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 172 VECACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 172 v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
+.-+|++.||..|-.+|.. . ...||-|+.++.
T Consensus 196 vl~~C~H~FC~~CI~~Wl~-------------------------~-~~tCPlCR~~~~ 227 (238)
T PHA02929 196 ILSNCNHVFCIECIDIWKK-------------------------E-KNTCPVCRTPFI 227 (238)
T ss_pred ecCCCCCcccHHHHHHHHh-------------------------c-CCCCCCCCCEee
Confidence 3446999999999765321 1 147999998875
No 182
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.28 E-value=25 Score=40.58 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=23.8
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCce-----eecccccc
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQA-----FCWLCGGA 252 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~-----FCw~C~~~ 252 (532)
-.||+|..++.-...=+.+.|. ||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 4788888887633333568895 8876 58888765
No 183
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.09 E-value=13 Score=41.75 Aligned_cols=36 Identities=25% Similarity=0.719 Sum_probs=28.4
Q ss_pred ccccccccccccc--cCceecCCCCcccHHHHHHHHHh
Q 009562 58 TVMCDICMEEVAG--DKATKMDCGHCFCNDCWTEHFIV 93 (532)
Q Consensus 58 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~ 93 (532)
-..|+||+..|-. -.++++.|||..|.-|.......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 4579999887543 35788999999999999876553
No 184
>smart00336 BBOX B-Box-type zinc finger.
Probab=37.45 E-value=32 Score=23.71 Aligned_cols=27 Identities=33% Similarity=0.816 Sum_probs=23.6
Q ss_pred cCCCCCC-cceeecCCCCeeEec-cCceeecccccc
Q 009562 219 KPCPKCH-KPVEKNGGCNLVSCI-CGQAFCWLCGGA 252 (532)
Q Consensus 219 K~CPkC~-~~IEKn~GCnhMtC~-C~~~FCw~C~~~ 252 (532)
..|+.|. .++. ++|. |....|..|...
T Consensus 4 ~~C~~h~~~~~~-------~~C~~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCEECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceE-------EECCCCCcccccccChh
Confidence 5799998 8888 9995 999999999865
No 185
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=37.26 E-value=13 Score=28.34 Aligned_cols=45 Identities=22% Similarity=0.510 Sum_probs=31.4
Q ss_pred cccccccccccccCceecCCC--CcccHHHHHHHHHhhhccCCcccccccccccccccC
Q 009562 59 VMCDICMEEVAGDKATKMDCG--HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICD 115 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~ 115 (532)
-.|..|-.+++.+..-..-|. ..||.+|-...+. -.||. |+..+.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN----------GVCPN--CGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc----------CcCcC--CCCccc
Confidence 468889888876654444454 5799999887653 26888 876543
No 186
>PHA02926 zinc finger-like protein; Provisional
Probab=36.37 E-value=7.6 Score=38.07 Aligned_cols=35 Identities=31% Similarity=0.767 Sum_probs=23.2
Q ss_pred cCCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 175 ACGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 175 ~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
+|+|.||+.|-..|... .. + ....+.||-|+....
T Consensus 196 ~CnHsFCl~CIr~Wr~~------------r~-~-------~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 196 SCNHIFCITCINIWHRT------------RR-E-------TGASDNCPICRTRFR 230 (242)
T ss_pred CCCchHHHHHHHHHHHh------------cc-c-------cCcCCcCCCCcceee
Confidence 59999999997755321 10 0 012378999998775
No 187
>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=35.98 E-value=34 Score=22.28 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.1
Q ss_pred CCCCCCcceeecCCCCeeEe
Q 009562 220 PCPKCHKPVEKNGGCNLVSC 239 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC 239 (532)
.||.|+..+.+..|=-+++|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999888667777
No 188
>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=35.82 E-value=16 Score=28.68 Aligned_cols=37 Identities=22% Similarity=0.541 Sum_probs=19.2
Q ss_pred ccccccccccccccccCc-ee-cCCCCcccHHHHHHHHH
Q 009562 56 SSTVMCDICMEEVAGDKA-TK-MDCGHCFCNDCWTEHFI 92 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~-~~-l~CgH~fC~~C~~~yl~ 92 (532)
.+...|.+|...|..... .. -.||+.||.+|....+.
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEc
Confidence 456789999999864221 12 27999999999866553
No 189
>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=35.76 E-value=3.8e+02 Score=31.10 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 009562 376 HLFEDQQQQLEANVEKLSKFLE 397 (532)
Q Consensus 376 ~lfe~~q~~lE~~~E~L~~~le 397 (532)
.+|.++-.++....+.|.+.+.
T Consensus 272 ~vFr~l~~q~~~m~esver~~~ 293 (683)
T PF08580_consen 272 IVFRNLGRQAQKMCESVERSLS 293 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4677766666666666666554
No 190
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=35.61 E-value=31 Score=25.49 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=17.1
Q ss_pred ccCCC--CCCcceeecCCCCeeEe-ccCc
Q 009562 218 TKPCP--KCHKPVEKNGGCNLVSC-ICGQ 243 (532)
Q Consensus 218 tK~CP--kC~~~IEKn~GCnhMtC-~C~~ 243 (532)
-+.|| .|+.-+--..--|-.+| +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 47999 99997654444567788 6875
No 191
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=35.10 E-value=15 Score=37.24 Aligned_cols=32 Identities=28% Similarity=0.744 Sum_probs=26.0
Q ss_pred cCCCCCCcceeecCCCCeeEe--ccCceeecccccccCCCC
Q 009562 219 KPCPKCHKPVEKNGGCNLVSC--ICGQAFCWLCGGATGRDH 257 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC--~C~~~FCw~C~~~~~~~H 257 (532)
-+|--|.-.|- +-| .|||.||++|-..+-..|
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~q 59 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQ 59 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCC
Confidence 57999998888 899 399999999988744433
No 192
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=34.72 E-value=29 Score=25.77 Aligned_cols=46 Identities=17% Similarity=0.492 Sum_probs=23.8
Q ss_pred cccccccccccccCcee-cCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 59 VMCDICMEEVAGDKATK-MDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
..|+|-+..+. -++. ..|.|.-|.| +..|+....+.+. .+||. |+.
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~---W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPK---WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCC---eECcC--CcC
Confidence 56888887754 3444 5999998864 6778877665544 79998 764
No 193
>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=34.68 E-value=73 Score=22.42 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=23.3
Q ss_pred cCCHHHHHHHHHHcCCChHHHHHHHHh
Q 009562 5 SLREHHARTLLIHYRWDVEKLLAVLVE 31 (532)
Q Consensus 5 ~i~~~~a~~LL~~~~W~~~~l~~~~~~ 31 (532)
+++++.-...|+.+++|++..++.+.+
T Consensus 14 ~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 14 DLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp SS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 478889999999999999999998874
No 194
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=34.37 E-value=6e+02 Score=27.11 Aligned_cols=81 Identities=19% Similarity=0.275 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccCCCC
Q 009562 372 EIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIENDLLGCLQLGTHNIARY 451 (532)
Q Consensus 372 ~~~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~~~~~~~~~~~~~ 451 (532)
+...++||.-|+.-+..+.=|.++|-. . ++..+|++.. .+..|++.||..|-+.=+ --+.+=+
T Consensus 216 E~MeqvFe~CQ~fE~~Rl~Ffkeil~~------------v-~~hldl~~~~--~~~~ly~eleqsIr~Ad~--eeDLrww 278 (472)
T KOG2856|consen 216 EDMEQVFEQCQQFEEKRLQFFKEILLK------------V-QRHLDLSRNS--SYSGLYRELEQSIRAADA--EEDLRWW 278 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH------------H-HHHhhhhhhc--chHHHHHHHHHHHhccch--HHHHHHH
Confidence 456689999998888777777666541 1 1223444332 334677777766653322 2344444
Q ss_pred CC-CCccccccccc--ccccc
Q 009562 452 QS-KGIERASELST--CWTSV 469 (532)
Q Consensus 452 ~~-~~~~~~~~~~~--~~~~~ 469 (532)
|+ -||..|..-|. .|++.
T Consensus 279 ~s~hG~~mamnWPqF~E~s~d 299 (472)
T KOG2856|consen 279 RSNHGPGMAMNWPQFEEWSPD 299 (472)
T ss_pred HhcCCCccccCCchHhhcChh
Confidence 44 45665555544 45443
No 195
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=34.29 E-value=9.8e+02 Score=29.62 Aligned_cols=74 Identities=20% Similarity=0.257 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCC------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 009562 368 DEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYP------DDKVMEIRMQVINLSVITDTLCKKMYECIENDLLGCL 441 (532)
Q Consensus 368 ~~~~~~~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~------~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e~~l~~~~ 441 (532)
.+..+.....|+.+..+|...+|.|... |..|..++ ..++..+..+...|.+++..+.+++.+--|.+++|.+
T Consensus 1224 ~~~i~~l~~~~~~lr~~l~~~~e~L~~~-E~~Lsdi~~~~~~a~~~LesLq~~~~~l~~~~keL~e~~~~ik~sdi~GA~ 1302 (1758)
T KOG0994|consen 1224 AEDIAQLASATESLRRQLQALTEDLPQE-EETLSDITNSLPLAGKDLESLQREFNGLLTTYKELREQLEKIKESDILGAF 1302 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhh-hhhhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCchhHH
Confidence 3344455567777777777777777654 33333221 2345566666666666666666666666666666655
Q ss_pred h
Q 009562 442 Q 442 (532)
Q Consensus 442 ~ 442 (532)
.
T Consensus 1303 ~ 1303 (1758)
T KOG0994|consen 1303 N 1303 (1758)
T ss_pred H
Confidence 4
No 196
>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=34.19 E-value=17 Score=27.33 Aligned_cols=22 Identities=27% Similarity=0.772 Sum_probs=13.2
Q ss_pred eeeeec-CCCeeecCcccCCCCC
Q 009562 170 CEVECA-CGAQFCFSCLSEAHSP 191 (532)
Q Consensus 170 ~~v~C~-C~~~fC~~C~~~~H~p 191 (532)
....|+ |+..||..|-.-.|.-
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 457896 9999999998777764
No 197
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=34.09 E-value=46 Score=27.22 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=20.7
Q ss_pred cccccccccccccc---cCceec--CCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 57 STVMCDICMEEVAG---DKATKM--DCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 57 ~~~~C~IC~e~~~~---~~~~~l--~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
....|.||-|++.. .++|.. .|+-..|+.|+.- ..++|. -.||+ |+...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY----Erkeg~---q~Cpq--Ckt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY----ERKEGN---QVCPQ--CKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH----HHHTS----SB-TT--T--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHH----HhhcCc---ccccc--cCCCc
Confidence 35679999999653 344543 7999999999754 345565 47888 77543
No 198
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.08 E-value=11 Score=37.92 Aligned_cols=37 Identities=22% Similarity=0.264 Sum_probs=24.8
Q ss_pred ccccccccccc-cccc-cCc-eecCCCCcccHHHHHHHHH
Q 009562 56 SSTVMCDICME-EVAG-DKA-TKMDCGHCFCNDCWTEHFI 92 (532)
Q Consensus 56 ~~~~~C~IC~e-~~~~-~~~-~~l~CgH~fC~~C~~~yl~ 92 (532)
....++++++. +... .+. +.-.|||.||..|-.-+..
T Consensus 93 ~~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~ 132 (271)
T COG5574 93 NREETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSI 132 (271)
T ss_pred ccccccccccCcccccccccceeeecccccchhhhHHHHH
Confidence 35678999988 4221 223 3348999999999666554
No 199
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=34.07 E-value=14 Score=37.49 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=22.2
Q ss_pred CccCCCCCCcceee-cCCCCeeEe-ccCcee
Q 009562 217 HTKPCPKCHKPVEK-NGGCNLVSC-ICGQAF 245 (532)
Q Consensus 217 ~tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 245 (532)
.|-+||.|+..+-+ .-+=|...| +|+|+|
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 36789999998875 457777888 488876
No 200
>cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. 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. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=34.04 E-value=4.3e+02 Score=25.33 Aligned_cols=53 Identities=9% Similarity=0.217 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 382 QQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 434 (532)
Q Consensus 382 q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 434 (532)
.+.++...|.....+.+++..+..++..++|.-+.++...--.+++++++.-|
T Consensus 143 v~~a~~~~e~~~~~~~~E~~rF~~~K~~d~k~~l~~~a~~qi~~~~~~~~~We 195 (200)
T cd07624 143 VEKLQDKLECANADLKADLERWKQNKRQDLKKILLDMAEKQIQYYEQCLAAWE 195 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444545555555555566666666666666666666666555
No 201
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.95 E-value=28 Score=26.95 Aligned_cols=6 Identities=67% Similarity=2.084 Sum_probs=3.4
Q ss_pred CCCCCC
Q 009562 220 PCPKCH 225 (532)
Q Consensus 220 ~CPkC~ 225 (532)
.||+|+
T Consensus 29 ~CPnCG 34 (61)
T COG2888 29 PCPNCG 34 (61)
T ss_pred eCCCCC
Confidence 555555
No 202
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=33.85 E-value=36 Score=28.00 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=23.9
Q ss_pred ccccccccccccc-cCc-eec-CCCCcccHHHHHHHHHh
Q 009562 58 TVMCDICMEEVAG-DKA-TKM-DCGHCFCNDCWTEHFIV 93 (532)
Q Consensus 58 ~~~C~IC~e~~~~-~~~-~~l-~CgH~fC~~C~~~yl~~ 93 (532)
..+|+-|.-.... ++. +.- -|.|.|..-|+..++.+
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh
Confidence 3456666543222 222 222 69999999999999998
No 203
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=33.55 E-value=32 Score=39.40 Aligned_cols=49 Identities=33% Similarity=0.645 Sum_probs=35.3
Q ss_pred cccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 57 STVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
..+.|.||--.+...-.+...|+|.-..+|+..||.. |. .||. +|+..+
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~----gd----~Cps-GCGC~C 1075 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT----GD----VCPS-GCGCHC 1075 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc----CC----cCCC-CCCcCc
Confidence 3466888876666555666789999999999999986 22 6875 344433
No 204
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.52 E-value=31 Score=29.67 Aligned_cols=27 Identities=26% Similarity=0.693 Sum_probs=15.6
Q ss_pred ccCCCCCCcce---eecCCCCeeEe-ccCce
Q 009562 218 TKPCPKCHKPV---EKNGGCNLVSC-ICGQA 244 (532)
Q Consensus 218 tK~CPkC~~~I---EKn~GCnhMtC-~C~~~ 244 (532)
.-.||+|+... ....|=-|..| .||+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 35799999322 22334456777 36654
No 205
>PRK12495 hypothetical protein; Provisional
Probab=32.39 E-value=46 Score=32.67 Aligned_cols=27 Identities=26% Similarity=0.720 Sum_probs=20.0
Q ss_pred CccCCCCCCcceeecCCCCeeEeccCceeecccccc
Q 009562 217 HTKPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGA 252 (532)
Q Consensus 217 ~tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~ 252 (532)
..+.||.|+.||-+..|| .||-.|...
T Consensus 41 sa~hC~~CG~PIpa~pG~---------~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ---------EFCPTCQQP 67 (226)
T ss_pred chhhcccccCcccCCCCe---------eECCCCCCc
Confidence 358999999999977776 555555544
No 206
>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=32.22 E-value=33 Score=22.34 Aligned_cols=24 Identities=29% Similarity=0.778 Sum_probs=12.6
Q ss_pred cCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 219 KPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 219 K~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
++||+|..+|++ .+|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 579999999975 345445555 353
No 207
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=31.90 E-value=23 Score=28.99 Aligned_cols=54 Identities=22% Similarity=0.633 Sum_probs=19.7
Q ss_pred CCCceEEeccccceeeeec-CCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCcceeecCCCC
Q 009562 157 HCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVEKNGGCN 235 (532)
Q Consensus 157 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IEKn~GCn 235 (532)
-|+--|........-|-|. |+...|..|.. +. ++...+.||.|+.+..+..|+-
T Consensus 14 iCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE----------YE---------------rkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 14 ICGDDVGLTENGEVFVACHECAFPVCRPCYE----------YE---------------RKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp SS--B--B-SSSSB--S-SSS-----HHHHH----------HH---------------HHTS-SB-TTT--B----TT--
T ss_pred cccCccccCCCCCEEEEEcccCCccchhHHH----------HH---------------hhcCcccccccCCCcccccCCC
Confidence 5777777666555667885 98888877643 11 2235589999999988776653
No 208
>PRK11827 hypothetical protein; Provisional
Probab=30.93 E-value=44 Score=26.02 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=17.2
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCc
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQ 243 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~ 243 (532)
-.||.|+.+++-..+=+.+.|+ |+.
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 5799999998865544556663 543
No 209
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=30.93 E-value=3.4e+02 Score=25.72 Aligned_cols=60 Identities=13% Similarity=0.218 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 374 KQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 434 (532)
Q Consensus 374 ~~~lfe~~q~~lE~~~E~L~~~le~~~~~~~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~e 434 (532)
...+++.+.+.++..+++|.+.++.--+..-.-.+-.-|+++.++.+-+.++-..|-+ +|
T Consensus 86 R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr~e~ee~~~~l~~le~~~~~-~e 145 (175)
T PRK13182 86 DFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEEMLERLQKLEARLKK-LE 145 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhHHHHHHHHHHHHHHHHHHHH-HH
Confidence 4578888888999999888888874322222223456677888777777665555444 44
No 210
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.74 E-value=31 Score=35.89 Aligned_cols=48 Identities=21% Similarity=0.561 Sum_probs=32.3
Q ss_pred ccccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 56 SSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 56 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
++...|.||-..++ -...+||+|..|.-|--..=.-- ..-.||. |+..
T Consensus 59 Een~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~RlRALY------~~K~C~~--CrTE 106 (493)
T COG5236 59 EENMNCQICAGSTT--YSARYPCGHQICHACAVRLRALY------MQKGCPL--CRTE 106 (493)
T ss_pred cccceeEEecCCce--EEEeccCCchHHHHHHHHHHHHH------hccCCCc--cccc
Confidence 45678999998755 34456999999999965532111 1236887 7753
No 211
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=30.72 E-value=5.1e+02 Score=25.19 Aligned_cols=52 Identities=15% Similarity=0.206 Sum_probs=28.8
Q ss_pred HhhhhhhHHHHHHHHHHHHHHHHHHhhhhccccch---hHHHHHHHHHHHHHHhh
Q 009562 295 YKAHTDSFKLESKLKETVLEKVSISEERESRLRDF---SWVTNGLYRLFRSRRVL 346 (532)
Q Consensus 295 ~~~h~~s~k~e~~l~~~i~~k~~~~~~~~~~~~~~---~~l~~a~~~l~~~R~vL 346 (532)
|..|..++..+.+-.+.+.+.+.++...-..+.++ .|+..|++.+.++.-..
T Consensus 38 ~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ag~~~~a~QEyvEA~~l~ 92 (204)
T COG2178 38 FLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPELYFAGFVTTALQEYVEATLLY 92 (204)
T ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhcchHHHHHHHHHHH
Confidence 45676665544333334444555554322223333 47899999998876554
No 212
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=29.51 E-value=60 Score=22.04 Aligned_cols=12 Identities=33% Similarity=0.515 Sum_probs=9.0
Q ss_pred ccCCCCCCccee
Q 009562 218 TKPCPKCHKPVE 229 (532)
Q Consensus 218 tK~CPkC~~~IE 229 (532)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 368998887665
No 213
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.35 E-value=41 Score=25.16 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=23.7
Q ss_pred ccccccccccccCceecCCCCcccHHHHHHH
Q 009562 60 MCDICMEEVAGDKATKMDCGHCFCNDCWTEH 90 (532)
Q Consensus 60 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 90 (532)
.|.||-..+..-..+.+.=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999998775455667778 8999999875
No 214
>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=29.19 E-value=40 Score=29.35 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=16.0
Q ss_pred cCCCCCCcceeecCCCCeeEec-cCcee
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCI-CGQAF 245 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~-C~~~F 245 (532)
-.||+|+.-.-=.+|= .+.|. |+|+|
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCC-eeECccccccc
Confidence 4799999877655553 24453 55443
No 215
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.56 E-value=48 Score=24.04 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=4.4
Q ss_pred CCCCCCcce
Q 009562 220 PCPKCHKPV 228 (532)
Q Consensus 220 ~CPkC~~~I 228 (532)
+||.|+..|
T Consensus 21 rC~~CG~rI 29 (44)
T smart00659 21 RCRECGYRI 29 (44)
T ss_pred ECCCCCceE
Confidence 455555444
No 216
>PF14149 YhfH: YhfH-like protein
Probab=28.32 E-value=4.4 Score=28.26 Aligned_cols=26 Identities=31% Similarity=0.790 Sum_probs=20.3
Q ss_pred cCccCCCCCCcceeecCCCCeeEe-cc
Q 009562 216 VHTKPCPKCHKPVEKNGGCNLVSC-IC 241 (532)
Q Consensus 216 ~~tK~CPkC~~~IEKn~GCnhMtC-~C 241 (532)
...|.||.|+..|+--.-|..+.| +|
T Consensus 11 Lp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 346999999999987777777777 45
No 217
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.29 E-value=39 Score=34.25 Aligned_cols=22 Identities=45% Similarity=1.091 Sum_probs=16.0
Q ss_pred ccCCCCCCcceee--cCCCCeeEe
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC 239 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC 239 (532)
-++||.|+.+|++ .+|=.-.+|
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~C 258 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFC 258 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEEC
Confidence 3799999999986 456444444
No 218
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.19 E-value=21 Score=39.00 Aligned_cols=28 Identities=36% Similarity=0.794 Sum_probs=20.4
Q ss_pred ccCCCCCCcceeecCCCCeeEec--cCceeecccccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCI--CGQAFCWLCGGA 252 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~--C~~~FCw~C~~~ 252 (532)
-..||-|-.+-. .-++ |||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 368999998766 4452 888888888644
No 219
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=27.85 E-value=91 Score=23.21 Aligned_cols=45 Identities=18% Similarity=0.410 Sum_probs=24.0
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccChHHH
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDEAVV 119 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~~~i 119 (532)
.|.||.|...++.. . +..++...=... ...+.||. |...+....+
T Consensus 2 ~f~CP~C~~~~~~~---~-----------L~~H~~~~H~~~-~~~v~CPi--C~~~~~~~l~ 46 (54)
T PF05605_consen 2 SFTCPYCGKGFSES---S-----------LVEHCEDEHRSE-SKNVVCPI--CSSRVTDNLI 46 (54)
T ss_pred CcCCCCCCCccCHH---H-----------HHHHHHhHCcCC-CCCccCCC--chhhhhhHHH
Confidence 57899998854411 1 223333221111 23589998 8765544333
No 220
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=27.76 E-value=54 Score=25.83 Aligned_cols=14 Identities=43% Similarity=0.949 Sum_probs=11.0
Q ss_pred CccCCCCCCcceee
Q 009562 217 HTKPCPKCHKPVEK 230 (532)
Q Consensus 217 ~tK~CPkC~~~IEK 230 (532)
+.|+||.|+..+..
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 45999999987664
No 221
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=27.34 E-value=53 Score=33.90 Aligned_cols=50 Identities=18% Similarity=0.485 Sum_probs=35.0
Q ss_pred ccccccccccccc-ccCceecCCCCcccHHHHHHHHHhhhccCCcccccccccccccc
Q 009562 57 STVMCDICMEEVA-GDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAI 113 (532)
Q Consensus 57 ~~~~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~ 113 (532)
.-|.|||=-+.-. .+.|+.|.|||..=+.=+...= ++|. ..++||- |+..
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~-~~FKCPY--CP~~ 385 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGV-LSFKCPY--CPEM 385 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCc-EEeeCCC--CCcc
Confidence 4689999776643 3457788999998876654432 3454 5799998 8754
No 222
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.32 E-value=42 Score=34.16 Aligned_cols=25 Identities=40% Similarity=1.060 Sum_probs=20.2
Q ss_pred ccCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
-++|+.|+.+|+| -+|=+-.+| .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4799999999997 578777777 375
No 223
>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=27.30 E-value=1e+02 Score=21.67 Aligned_cols=27 Identities=26% Similarity=0.292 Sum_probs=24.1
Q ss_pred cCCHHHHHHHHHHcCCChHHHHHHHHh
Q 009562 5 SLREHHARTLLIHYRWDVEKLLAVLVE 31 (532)
Q Consensus 5 ~i~~~~a~~LL~~~~W~~~~l~~~~~~ 31 (532)
+++...++..|..+++|++..++.+.+
T Consensus 15 ~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 15 NLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 578889999999999999999998874
No 224
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=27.24 E-value=3.4e+02 Score=29.13 Aligned_cols=18 Identities=6% Similarity=0.062 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009562 415 VINLSVITDTLCKKMYEC 432 (532)
Q Consensus 415 ~~~l~~~~~~~~~~l~~~ 432 (532)
+.-|.+-|+..|..+++.
T Consensus 364 LdpLerqVre~Fh~IV~s 381 (389)
T PF05633_consen 364 LDPLERQVREVFHRIVRS 381 (389)
T ss_pred cHHHHHHHHHHHHHHHHh
Confidence 335666666666666554
No 225
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.23 E-value=52 Score=29.75 Aligned_cols=21 Identities=48% Similarity=1.211 Sum_probs=16.0
Q ss_pred CCCCceEEeccccceeeeecCCCeeecC
Q 009562 156 PHCGNAIRVEEVEVCEVECACGAQFCFS 183 (532)
Q Consensus 156 p~C~~~i~~~~~~~~~v~C~C~~~fC~~ 183 (532)
|.|++... .+.|.||..+|..
T Consensus 81 P~CGn~~~-------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 81 PHCGNQYA-------FAVCGCGKLFCID 101 (131)
T ss_pred CCCcChhc-------EEEecCCCEEEeC
Confidence 47887643 3688999999976
No 226
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=27.18 E-value=66 Score=30.01 Aligned_cols=36 Identities=28% Similarity=0.572 Sum_probs=22.7
Q ss_pred ccccccccccccccCceecC-------CCCccc------HHHHHHHHHhhh
Q 009562 58 TVMCDICMEEVAGDKATKMD-------CGHCFC------NDCWTEHFIVKI 95 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~-------CgH~fC------~~C~~~yl~~~i 95 (532)
..+|+||+|- +-+.+.|- |.-+.| .+|+.+|-....
T Consensus 2 d~~CpICme~--PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEH--PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccC--CCceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 4689999986 33555443 333334 578888876544
No 227
>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=27.14 E-value=43 Score=33.97 Aligned_cols=22 Identities=41% Similarity=0.958 Sum_probs=16.7
Q ss_pred ccCCCCCCcceee--cCCCCeeEe
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC 239 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC 239 (532)
-++||.|+.+|++ .+|=.-.+|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~C 268 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFC 268 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEEC
Confidence 3699999999996 566555555
No 228
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=27.03 E-value=44 Score=33.95 Aligned_cols=25 Identities=40% Similarity=1.024 Sum_probs=18.1
Q ss_pred ccCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 3699999999986 566555566 355
No 229
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=26.83 E-value=43 Score=26.52 Aligned_cols=17 Identities=24% Similarity=0.702 Sum_probs=12.2
Q ss_pred cccHHHHHHHHHhhhcc
Q 009562 81 CFCNDCWTEHFIVKINE 97 (532)
Q Consensus 81 ~fC~~C~~~yl~~~i~~ 97 (532)
-||++|+..|+..+-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999887654
No 230
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.82 E-value=43 Score=33.99 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=18.2
Q ss_pred ccCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
.++||+|+.+|++ .+|=.-.+| .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 4799999999986 566555555 354
No 231
>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=26.43 E-value=37 Score=30.45 Aligned_cols=25 Identities=12% Similarity=0.215 Sum_probs=16.0
Q ss_pred cCCCCCCcceeecCCCCeeEe-ccCce
Q 009562 219 KPCPKCHKPVEKNGGCNLVSC-ICGQA 244 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC-~C~~~ 244 (532)
+.||+|++..---.- +-++| +||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCc
Confidence 689999986652111 55777 46665
No 232
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.31 E-value=45 Score=34.04 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=18.9
Q ss_pred ccCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 4799999999986 567666666 365
No 233
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=25.99 E-value=4.7e+02 Score=28.19 Aligned_cols=88 Identities=23% Similarity=0.308 Sum_probs=54.4
Q ss_pred HHHHhhhhhHHHHHHhhhhhhHHHHHH-HHHHHHHHHHHHhhhhccccchhHHHHHHHHHHH-HHHhhhccccceeeccc
Q 009562 281 AKRELYRYMHYHNRYKAHTDSFKLESK-LKETVLEKVSISEERESRLRDFSWVTNGLYRLFR-SRRVLSYSYPFAFYMFG 358 (532)
Q Consensus 281 ~~~~l~ry~~y~~R~~~h~~s~k~e~~-l~~~i~~k~~~~~~~~~~~~~~~~l~~a~~~l~~-~R~vL~~Sy~~~yy~~~ 358 (532)
||.++--...--.|++.|-+.++-|-. |.+.++.+-++.++ |+.-.-+|.+ ||+|..
T Consensus 123 AKDSItSlKekt~~vnQHVq~LQseCsvlsEnLErrrQEaeE----------LEgyCsqLk~nCrkVt~----------- 181 (558)
T PF15358_consen 123 AKDSITSLKEKTSRVNQHVQTLQSECSVLSENLERRRQEAEE----------LEGYCSQLKENCRKVTR----------- 181 (558)
T ss_pred cccchhhHHHhhHHHHHHHHHHHHHhHHHHHHHHhhhhHHHH----------HHHHHHHHHHHHHHHhh-----------
Confidence 444444444455688889888887744 55666555554444 4445555554 444441
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009562 359 EELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLE 397 (532)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~~~le 397 (532)
+-++.+++.+.+...-.-||..+--|...|.
T Consensus 182 --------SVedaEiKtnvLkqnS~~LEekLr~lq~qLq 212 (558)
T PF15358_consen 182 --------SVEDAEIKTNVLKQNSALLEEKLRYLQQQLQ 212 (558)
T ss_pred --------hHHHHHHHhcccccchHHHHHHHHHHHHHhc
Confidence 1233456778888888888888877777776
No 234
>PF08926 DUF1908: Domain of unknown function (DUF1908); InterPro: IPR015022 This domain is found in microtubule-associated serine/threonine-protein kinases. ; GO: 0000287 magnesium ion binding, 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1V9V_A.
Probab=25.97 E-value=4.1e+02 Score=27.07 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 009562 375 QHLFEDQQQQLEANVEKLSKF 395 (532)
Q Consensus 375 ~~lfe~~q~~lE~~~E~L~~~ 395 (532)
...|-.+|+.||+-+++-.+.
T Consensus 186 s~YF~ElsEnLekLl~ea~er 206 (282)
T PF08926_consen 186 SRYFYELSENLEKLLQEAHER 206 (282)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhcccC
Confidence 356777777777665544443
No 235
>PRK10445 endonuclease VIII; Provisional
Probab=25.30 E-value=50 Score=33.38 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=18.5
Q ss_pred ccCCCCCCcceee--cCCCCeeEe-ccC
Q 009562 218 TKPCPKCHKPVEK--NGGCNLVSC-ICG 242 (532)
Q Consensus 218 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 242 (532)
-++||.|+.+|++ .+|=.-.+| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 4799999999986 567555666 354
No 236
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=25.10 E-value=57 Score=28.17 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=20.1
Q ss_pred CCCCcccHHHHHHHHHhhhccCCcccccccc
Q 009562 77 DCGHCFCNDCWTEHFIVKINEGQSKRIRCMA 107 (532)
Q Consensus 77 ~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~ 107 (532)
.|.|.|..-|+..++.+. -.||.
T Consensus 80 ~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc--------CcCCC
Confidence 699999999999999872 47887
No 237
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.98 E-value=26 Score=28.13 Aligned_cols=44 Identities=23% Similarity=0.545 Sum_probs=30.5
Q ss_pred cccccccccccccCceecCC--CCcccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 59 VMCDICMEEVAGDKATKMDC--GHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~C--gH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
..|..|--+++++..-.+-| .|.||.+|-..-+. =.||. |+..+
T Consensus 6 PnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~----------g~CPn--CGGel 51 (84)
T COG3813 6 PNCECCDRDLPPDSTDARICTFECTFCADCAENRLH----------GLCPN--CGGEL 51 (84)
T ss_pred CCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc----------CcCCC--CCchh
Confidence 35888888887655444555 48899999876543 25888 88655
No 238
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=24.50 E-value=51 Score=22.72 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=16.0
Q ss_pred ccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 82 FCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 82 fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
.|.+|.++|....-.-=....+.|+. |+-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCE
Confidence 48899999976532211235688987 76543
No 239
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=24.47 E-value=26 Score=29.23 Aligned_cols=35 Identities=29% Similarity=0.503 Sum_probs=28.9
Q ss_pred cCCCCCCcceeecCCCCeeEeccCceeecccccccCCC
Q 009562 219 KPCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGATGRD 256 (532)
Q Consensus 219 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~~~~ 256 (532)
.-||.|+.| .+.|--+.+.|++.|=..|...|-..
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHcc
Confidence 468888887 46788888899999999999997543
No 240
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=24.40 E-value=8.1e+02 Score=25.39 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=5.0
Q ss_pred ChhhhHHHHh
Q 009562 193 SCSMWDLWAK 202 (532)
Q Consensus 193 ~C~~~~~w~~ 202 (532)
.|.+..+++.
T Consensus 76 ~c~EL~~~I~ 85 (325)
T PF08317_consen 76 SCRELKKYIS 85 (325)
T ss_pred HHHHHHHHHH
Confidence 4555555544
No 241
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.20 E-value=96 Score=28.83 Aligned_cols=32 Identities=28% Similarity=0.530 Sum_probs=19.7
Q ss_pred cccccccCCCCCCCCceEEeccccceeeeec-CCCe
Q 009562 145 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 179 (532)
Q Consensus 145 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 179 (532)
.++.+..|| .|+.-+...+.-...+.|| ||..
T Consensus 105 ~~~~~Y~Cp---~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICP---NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECC---CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345666898 5776565554333457776 7765
No 242
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.09 E-value=59 Score=28.54 Aligned_cols=27 Identities=26% Similarity=0.591 Sum_probs=18.1
Q ss_pred cCCCCCCcceee--cCCCCeeEec-cCcee
Q 009562 219 KPCPKCHKPVEK--NGGCNLVSCI-CGQAF 245 (532)
Q Consensus 219 K~CPkC~~~IEK--n~GCnhMtC~-C~~~F 245 (532)
+-||+|+.++.- .++=+-+.|+ ||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 689999988764 2122268884 88764
No 243
>KOG2150 consensus CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=24.00 E-value=1.1e+03 Score=26.70 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 370 EREIKQHLFEDQQQQLEANVEKLSK 394 (532)
Q Consensus 370 ~~~~~~~lfe~~q~~lE~~~E~L~~ 394 (532)
++......+..+...||++++.+.-
T Consensus 119 ek~d~~~wi~~~ideLe~q~d~~ea 143 (575)
T KOG2150|consen 119 EKRDTMDWISNQIDELERQVDSFEA 143 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445566667777777777766544
No 244
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.76 E-value=26 Score=40.76 Aligned_cols=57 Identities=25% Similarity=0.288 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHH-hhcccCCC---CchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 377 LFEDQQQQLEANVEKLSKF-LEEPFDQY---PDDKVMEIRMQVINLSVITDTLCKKMYECI 433 (532)
Q Consensus 377 lfe~~q~~lE~~~E~L~~~-le~~~~~~---~~~~i~~~k~~~~~l~~~~~~~~~~l~~~~ 433 (532)
|=.+.=..+--.+|+|.++ -++++... .++.|..+|.+-+-++.-...++-+.-+.|
T Consensus 776 lTHfrP~EIgvsvEkLrELGY~~Di~G~pL~~~dQivELk~QDIils~~aaeyllkva~FI 836 (900)
T PF03833_consen 776 LTHFRPREIGVSVEKLRELGYTHDIYGKPLESDDQIVELKVQDIILSEDAAEYLLKVAKFI 836 (900)
T ss_dssp -------------------------------------------------------------
T ss_pred cccccHHhcCCCHHHHHHhCccccccCCccCCccceeEeehhcEecchhHHHHHHHHHHHH
Confidence 4444555677788888877 23344322 245566777666656555555544444444
No 245
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=23.42 E-value=48 Score=38.22 Aligned_cols=49 Identities=16% Similarity=0.374 Sum_probs=33.8
Q ss_pred ccccccccccccccCc-eecCCCCcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 58 TVMCDICMEEVAGDKA-TKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
.-.|++|+..+..... ....|+|.||..|+..|-..+ =.||. |...+..
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFGE 172 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhhhe
Confidence 3468999887653222 234899999999999986642 36887 6665543
No 246
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=23.42 E-value=72 Score=29.78 Aligned_cols=49 Identities=22% Similarity=0.442 Sum_probs=33.1
Q ss_pred cccccccccccccccCceecCCCC---cccHHHHHHHHHhhhccCCccccccccccccccc
Q 009562 57 STVMCDICMEEVAGDKATKMDCGH---CFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAIC 114 (532)
Q Consensus 57 ~~~~C~IC~e~~~~~~~~~l~CgH---~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~ 114 (532)
....|-||.++-. .......|.. ....+|+..|+... ...+|+. |+...
T Consensus 7 ~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPY 58 (162)
T ss_pred CCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeE
Confidence 4568999999843 1222224444 45899999999863 3478998 88755
No 247
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=23.36 E-value=1.1e+03 Score=26.57 Aligned_cols=78 Identities=14% Similarity=0.306 Sum_probs=41.0
Q ss_pred HHhhhccccceeeccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-ccCCCCchHHHHHHHHHHHHHHH
Q 009562 343 RRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEE-PFDQYPDDKVMEIRMQVINLSVI 421 (532)
Q Consensus 343 R~vL~~Sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~~~le~-~~~~~~~~~i~~~k~~~~~l~~~ 421 (532)
+.+|..++.||- ....+|.+-.++|..-....++.+. ++.+ -.+-+..++.++..|...
T Consensus 154 k~ll~~~~~~G~-------------------a~~~le~~l~~~e~~f~~f~~l~~~Gd~~~-A~e~l~~l~~~~~~l~~~ 213 (569)
T PRK04778 154 KSLLANRFSFGP-------------------ALDELEKQLENLEEEFSQFVELTESGDYVE-AREILDQLEEELAALEQI 213 (569)
T ss_pred HHHHhcCccccc-------------------hHHHHHHHHHHHHHHHHHHHHHhcCCCHHH-HHHHHHHHHHHHHHHHHH
Confidence 456777777771 2235666666666666666555552 1100 012245566666555555
Q ss_pred HHHHHHHHHHHHHhhhhhhh
Q 009562 422 TDTLCKKMYECIENDLLGCL 441 (532)
Q Consensus 422 ~~~~~~~l~~~~e~~l~~~~ 441 (532)
++.. =.||..+++.||+-|
T Consensus 214 ~~~i-P~l~~~~~~~~P~ql 232 (569)
T PRK04778 214 MEEI-PELLKELQTELPDQL 232 (569)
T ss_pred HHHH-HHHHHHHHHHhhHHH
Confidence 5432 245666666665444
No 248
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.25 E-value=29 Score=32.31 Aligned_cols=29 Identities=17% Similarity=0.494 Sum_probs=21.1
Q ss_pred cccccccccccccccccC-ceecCCCCccc
Q 009562 55 LSSTVMCDICMEEVAGDK-ATKMDCGHCFC 83 (532)
Q Consensus 55 ~~~~~~C~IC~e~~~~~~-~~~l~CgH~fC 83 (532)
.....+|.||+|++...+ +.+|+|-..|.
T Consensus 174 ~ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred cccCCcEEEEhhhccCCCceeccceEEEee
Confidence 346789999999987654 45679876654
No 249
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.30 E-value=1.2e+02 Score=27.62 Aligned_cols=18 Identities=28% Similarity=0.529 Sum_probs=11.9
Q ss_pred ccccccCCCCCCCCceEEecc
Q 009562 146 NKMVKWCPSTPHCGNAIRVEE 166 (532)
Q Consensus 146 ~~~~~~CP~~p~C~~~i~~~~ 166 (532)
+.....|| .|+.-+...+
T Consensus 96 ~~~~Y~Cp---~C~~~y~~~e 113 (147)
T smart00531 96 NNAYYKCP---NCQSKYTFLE 113 (147)
T ss_pred CCcEEECc---CCCCEeeHHH
Confidence 44566898 6987766543
No 251
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=21.96 E-value=2.7e+02 Score=28.79 Aligned_cols=31 Identities=19% Similarity=0.316 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhhhhHHHHHHhhhhhhHHHHH
Q 009562 276 KKTERAKRELYRYMHYHNRYKAHTDSFKLES 306 (532)
Q Consensus 276 ~~~~~~~~~l~ry~~y~~R~~~h~~s~k~e~ 306 (532)
.+..+|-+.|++|.+-.+|-.+....+.+|.
T Consensus 151 ~ranQAi~TLEkYk~~Ld~~~~~L~~lEled 181 (349)
T COG1623 151 SRANQAIQTLEKYKTVLDRVLNQLNLLELED 181 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhHHHhh
Confidence 4567788899999999988877766666653
No 252
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=21.95 E-value=64 Score=30.77 Aligned_cols=25 Identities=36% Similarity=0.844 Sum_probs=20.0
Q ss_pred CCCCCCcceeecCCCCeeEe-ccCcee
Q 009562 220 PCPKCHKPVEKNGGCNLVSC-ICGQAF 245 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC-~C~~~F 245 (532)
.||+|+.++.+ .+.|+|.| .|++..
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEE-CCCCEEECCCCCCEE
Confidence 79999999987 44599999 498643
No 253
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.89 E-value=6.3e+02 Score=24.77 Aligned_cols=30 Identities=17% Similarity=0.185 Sum_probs=18.6
Q ss_pred cccc-CCCCCCCCccccccccccccccCCCC
Q 009562 444 GTHN-IARYQSKGIERASELSTCWTSVNTTT 473 (532)
Q Consensus 444 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 473 (532)
+++. ++|..+--|-++.+.+..|.+...+.
T Consensus 92 gt~~e~app~~a~~p~~~aap~S~rs~~~g~ 122 (233)
T COG3416 92 GTPQEPAPPANAPPPKEPAAPPSWRSSPAGP 122 (233)
T ss_pred CCCCCCCCCcCCCCCCCCCCCCCccccccCC
Confidence 3444 66666544555677888887665553
No 254
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=21.87 E-value=97 Score=26.54 Aligned_cols=27 Identities=37% Similarity=0.795 Sum_probs=17.3
Q ss_pred ccCCCCCCCCceEEeccccc-eeeeec-CCCe
Q 009562 150 KWCPSTPHCGNAIRVEEVEV-CEVECA-CGAQ 179 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-C~~~ 179 (532)
.+|| .|++.+.++.+.. ..+.|. |.+.
T Consensus 2 ~FCP---~Cgn~Live~g~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP---TCGNMLIVESGESCNRFSCRTCPYV 30 (105)
T ss_pred cccC---CCCCEEEEecCCeEeeEEcCCCCce
Confidence 4788 6999998876543 344553 5444
No 255
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=21.84 E-value=52 Score=24.47 Aligned_cols=35 Identities=20% Similarity=0.523 Sum_probs=24.2
Q ss_pred cccccccccccccC--ceecCCCCcccHHHHHHHHHh
Q 009562 59 VMCDICMEEVAGDK--ATKMDCGHCFCNDCWTEHFIV 93 (532)
Q Consensus 59 ~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~ 93 (532)
..|.+|-..|.... ..--.||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 35888877765321 112379999999999887553
No 256
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.69 E-value=57 Score=25.06 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.7
Q ss_pred CccCCCCCCccee
Q 009562 217 HTKPCPKCHKPVE 229 (532)
Q Consensus 217 ~tK~CPkC~~~IE 229 (532)
+.-.||.|+.+..
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 4468999999988
No 257
>PRK10220 hypothetical protein; Provisional
Probab=21.67 E-value=67 Score=28.01 Aligned_cols=15 Identities=27% Similarity=0.689 Sum_probs=11.1
Q ss_pred cCCCCCCcceeecCC
Q 009562 219 KPCPKCHKPVEKNGG 233 (532)
Q Consensus 219 K~CPkC~~~IEKn~G 233 (532)
-.||+|..-.-=.+|
T Consensus 4 P~CP~C~seytY~d~ 18 (111)
T PRK10220 4 PHCPKCNSEYTYEDN 18 (111)
T ss_pred CcCCCCCCcceEcCC
Confidence 579999987665555
No 258
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.65 E-value=67 Score=22.59 Aligned_cols=29 Identities=31% Similarity=0.573 Sum_probs=17.5
Q ss_pred CCCCCCcceeecCCCCeeEeccCceeeccccccc
Q 009562 220 PCPKCHKPVEKNGGCNLVSCICGQAFCWLCGGAT 253 (532)
Q Consensus 220 ~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~~ 253 (532)
.||+|+..++...- ..+ ....|-.|++.|
T Consensus 1 ~CP~C~~~l~~~~~-~~~----~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDV----EIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEE-CCE----EEEECCCCCeEE
Confidence 59999998774332 111 234466677775
No 259
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.65 E-value=9e+02 Score=24.93 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=8.4
Q ss_pred hhccccceeecccc
Q 009562 346 LSYSYPFAFYMFGE 359 (532)
Q Consensus 346 L~~Sy~~~yy~~~~ 359 (532)
+-.+|+.-+|+...
T Consensus 103 ~~K~YV~P~~l~~~ 116 (300)
T KOG2629|consen 103 FVKSYVLPRFLGES 116 (300)
T ss_pred HHHHHHHHHhhCcc
Confidence 34467777776543
No 260
>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=21.63 E-value=98 Score=23.56 Aligned_cols=27 Identities=41% Similarity=0.815 Sum_probs=19.9
Q ss_pred cCCCCCCCCceEEecc-ccceeeeec-CCCee
Q 009562 151 WCPSTPHCGNAIRVEE-VEVCEVECA-CGAQF 180 (532)
Q Consensus 151 ~CP~~p~C~~~i~~~~-~~~~~v~C~-C~~~f 180 (532)
-|| .|+.-|.+++ .....+.|+ ||..+
T Consensus 4 ~CP---~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP---DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC---CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 577 7999998765 234567896 98875
No 261
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.56 E-value=48 Score=39.44 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=24.5
Q ss_pred cCccCCCCCCcceeecCCCCeeEec-cCc-----eeecccccc
Q 009562 216 VHTKPCPKCHKPVEKNGGCNLVSCI-CGQ-----AFCWLCGGA 252 (532)
Q Consensus 216 ~~tK~CPkC~~~IEKn~GCnhMtC~-C~~-----~FCw~C~~~ 252 (532)
...+.||.|+... ....|. ||. .||-.|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCc
Confidence 4568999999985 447895 985 599999766
No 262
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=21.31 E-value=8.8e+02 Score=24.71 Aligned_cols=53 Identities=23% Similarity=0.421 Sum_probs=33.4
Q ss_pred chhHHHHHHHHHHHHHHhhhccccceeeccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009562 328 DFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKF 395 (532)
Q Consensus 328 ~~~~l~~a~~~l~~~R~vL~~Sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~lE~~~E~L~~~ 395 (532)
++.||+..+..+.+++..+.- .++.+.+++.....++.....||...|+|.+.
T Consensus 167 kV~WLR~~L~Ei~Ea~e~~~~---------------~~~~e~eke~~~r~l~~~~~ELe~~~EeL~~~ 219 (269)
T PF05278_consen 167 KVDWLRSKLEEILEAKEIYDQ---------------HETREEEKEEKDRKLELKKEELEELEEELKQK 219 (269)
T ss_pred chHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 667999999999887776521 12234444555555666666666666666544
No 263
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=21.23 E-value=1.1e+02 Score=24.29 Aligned_cols=31 Identities=32% Similarity=0.623 Sum_probs=22.9
Q ss_pred ccCCCCCCCCceEEeccccceeeeec-CCCeeecC
Q 009562 150 KWCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFS 183 (532)
Q Consensus 150 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~ 183 (532)
+.|| +|++.-.+=+.....|.|. ||...+..
T Consensus 20 VkCp---dC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 20 VKCP---DCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EECC---CCCCEEEEeccCceEEEecccccEEEec
Confidence 5788 8998766555556678994 99987754
No 264
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=21.22 E-value=3.6e+02 Score=22.37 Aligned_cols=34 Identities=18% Similarity=0.238 Sum_probs=16.6
Q ss_pred hhhhHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Q 009562 286 YRYMHYHNRYKAHTDSFKLESKLKETVLEKVSIS 319 (532)
Q Consensus 286 ~ry~~y~~R~~~h~~s~k~e~~l~~~i~~k~~~~ 319 (532)
.||.....+|..|...++.-++=.+.|..||+.+
T Consensus 43 ~rl~~~~~~f~~~~~~l~~mK~DLd~i~krir~l 76 (88)
T PF10241_consen 43 QRLAEARERFARHTKLLKEMKKDLDYIFKRIRSL 76 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4666666666666655443322223344444433
No 265
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.98 E-value=1.1e+02 Score=29.01 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=18.5
Q ss_pred cccccccCCCCCCCCceEEeccccceeeeec-CCCe
Q 009562 145 DNKMVKWCPSTPHCGNAIRVEEVEVCEVECA-CGAQ 179 (532)
Q Consensus 145 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 179 (532)
.+..+..|| .|+.-+...+.-...+.|| ||..
T Consensus 113 ~~~~~Y~Cp---~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 113 ENNMFFFCP---NCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred cCCCEEECC---CCCcEEeHHHHhhcCCcCCCCCCC
Confidence 344566898 5886666555333345664 5544
No 266
>PF14353 CpXC: CpXC protein
Probab=20.96 E-value=41 Score=29.83 Aligned_cols=50 Identities=28% Similarity=0.606 Sum_probs=28.9
Q ss_pred ccccccccccccChHHHHHHhcCCChhHHHHHHHHHHHHhhhcccccccCCCCCCCCceEEec
Q 009562 103 IRCMAHKCNAICDEAVVRNLVSKKHPNLAEKFERFLLESFIEDNKMVKWCPSTPHCGNAIRVE 165 (532)
Q Consensus 103 i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~l~~~~v~~~~~~~~CP~~p~C~~~i~~~ 165 (532)
|+||. |+..+.......+-...+|++.++. +...-...-|| .||..+.+.
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~i--------l~g~l~~~~CP---~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEKI--------LDGSLFSFTCP---SCGHKFRLE 51 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHHH--------HcCCcCEEECC---CCCCceecC
Confidence 78998 8887765544333333445555432 12233445788 688877654
No 267
>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=20.91 E-value=56 Score=23.30 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=10.6
Q ss_pred eeeec-CCCeeecCccc
Q 009562 171 EVECA-CGAQFCFSCLS 186 (532)
Q Consensus 171 ~v~C~-C~~~fC~~C~~ 186 (532)
.+.|+ |+..||..+..
T Consensus 13 ~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp HEE-TTTS-EE-TTTHS
T ss_pred CeECCCCCcccCccccC
Confidence 47896 99999999764
No 268
>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=20.80 E-value=41 Score=24.90 Aligned_cols=44 Identities=23% Similarity=0.484 Sum_probs=22.0
Q ss_pred cccccccccccccCceecCCC-CcccHHHHHHHHHhhhccCCcccccccccccccccCh
Q 009562 59 VMCDICMEEVAGDKATKMDCG-HCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNAICDE 116 (532)
Q Consensus 59 ~~C~IC~e~~~~~~~~~l~Cg-H~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~~~~~ 116 (532)
+.|--|.-... --+.|. |+.|..|+...+.. .-.||. |+..+|.
T Consensus 3 ~nCKsCWf~~k----~Li~C~dHYLCl~CLt~ml~~--------s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFANK----GLIKCSDHYLCLNCLTLMLSR--------SDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S--S----SEEE-SS-EEEHHHHHHT-SS--------SSEETT--TTEE---
T ss_pred ccChhhhhcCC----CeeeecchhHHHHHHHHHhcc--------ccCCCc--ccCcCcc
Confidence 46777765422 233665 99999999987754 247888 8877654
No 269
>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=20.59 E-value=60 Score=18.83 Aligned_cols=16 Identities=31% Similarity=0.793 Sum_probs=12.6
Q ss_pred eecCcccCCCCCCChh
Q 009562 180 FCFSCLSEAHSPCSCS 195 (532)
Q Consensus 180 fC~~C~~~~H~p~~C~ 195 (532)
.|+.|++.-|.-..|.
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 5899999999866653
No 270
>PF15616 TerY-C: TerY-C metal binding domain
Probab=20.21 E-value=72 Score=28.86 Aligned_cols=35 Identities=31% Similarity=0.763 Sum_probs=19.3
Q ss_pred CccCCCCCCccee-ecCCCCeeEec--cCceeeccccc
Q 009562 217 HTKPCPKCHKPVE-KNGGCNLVSCI--CGQAFCWLCGG 251 (532)
Q Consensus 217 ~tK~CPkC~~~IE-Kn~GCnhMtC~--C~~~FCw~C~~ 251 (532)
..--||.|+...- -.-+|.+++|. =+...|--|+.
T Consensus 76 g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~ 113 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGN 113 (131)
T ss_pred CCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCC
Confidence 3468999998743 22345555552 33444445544
No 271
>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=20.18 E-value=44 Score=25.09 Aligned_cols=24 Identities=29% Similarity=0.703 Sum_probs=11.9
Q ss_pred CCCCCCcceeecCCC--CeeEe-ccCc
Q 009562 220 PCPKCHKPVEKNGGC--NLVSC-ICGQ 243 (532)
Q Consensus 220 ~CPkC~~~IEKn~GC--nhMtC-~C~~ 243 (532)
+|++|++.+-+.++= -.+.| +|+.
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCc
Confidence 566666665553221 24555 4553
No 272
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=20.18 E-value=71 Score=32.10 Aligned_cols=48 Identities=19% Similarity=0.367 Sum_probs=36.0
Q ss_pred ccccccccccccccCceecCCCCcccHHHHHHHHHhhhccCCccccccccccccc
Q 009562 58 TVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKCNA 112 (532)
Q Consensus 58 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~i~~g~~~~i~CP~~~C~~ 112 (532)
...|||=+-.+. ..+++-.|||.|=++=+..++... ..++||..+|..
T Consensus 176 s~rdPis~~~I~-nPviSkkC~HvydrDsI~~~l~~~------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIV-NPVISKKCGHVYDRDSIMQILCDE------ITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhh-chhhhcCcCcchhhhhHHHHhccC------ceeecccccCCc
Confidence 356888766543 245566999999999988887652 358999999994
No 273
>PLN02189 cellulose synthase
Probab=20.11 E-value=64 Score=38.70 Aligned_cols=59 Identities=27% Similarity=0.581 Sum_probs=40.6
Q ss_pred cCCCCCCCCceEEeccccceeeeec-CCCeeecCcccCCCCCCChhhhHHHHhhhhchHHHHHHHHcCccCCCCCCccee
Q 009562 151 WCPSTPHCGNAIRVEEVEVCEVECA-CGAQFCFSCLSEAHSPCSCSMWDLWAKKCRDESETVNWITVHTKPCPKCHKPVE 229 (532)
Q Consensus 151 ~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~e~~~~~~i~~~tK~CPkC~~~IE 229 (532)
-|. -|+--+....+...-|-|. |+...|..|.+- . .+...+.||.|+....
T Consensus 36 ~C~---iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey----------e---------------r~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCE---ICGDEIGLTVDGDLFVACNECGFPVCRPCYEY----------E---------------RREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccc---ccccccCcCCCCCEEEeeccCCCccccchhhh----------h---------------hhcCCccCcccCCchh
Confidence 465 5877777666556678996 999999988631 0 0123478999998888
Q ss_pred ecCCCCee
Q 009562 230 KNGGCNLV 237 (532)
Q Consensus 230 Kn~GCnhM 237 (532)
+--|++.+
T Consensus 88 r~kgs~~v 95 (1040)
T PLN02189 88 RLKGSPRV 95 (1040)
T ss_pred hccCCCCc
Confidence 66666553
No 274
>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=20.09 E-value=62 Score=24.64 Aligned_cols=13 Identities=23% Similarity=0.457 Sum_probs=10.2
Q ss_pred CccCCCCCCccee
Q 009562 217 HTKPCPKCHKPVE 229 (532)
Q Consensus 217 ~tK~CPkC~~~IE 229 (532)
+.-.||.|+.+..
T Consensus 25 ~l~~C~~cG~~~~ 37 (55)
T TIGR01031 25 TLVVCPNCGEFKL 37 (55)
T ss_pred cceECCCCCCccc
Confidence 3457999998887
No 275
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=20.06 E-value=44 Score=34.36 Aligned_cols=28 Identities=25% Similarity=0.776 Sum_probs=22.2
Q ss_pred ccCCCCCCcceeecCCCCeeEec---cCceeecccccc
Q 009562 218 TKPCPKCHKPVEKNGGCNLVSCI---CGQAFCWLCGGA 252 (532)
Q Consensus 218 tK~CPkC~~~IEKn~GCnhMtC~---C~~~FCw~C~~~ 252 (532)
..-|-+|..+|- ++=| |++-||+.|-..
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 468999999998 6553 888888888765
Done!