Query 048114
Match_columns 234
No_of_seqs 189 out of 1396
Neff 9.7
Searched_HMMs 46136
Date Fri Mar 29 06:23:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048114.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048114hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 7.1E-36 1.5E-40 250.3 11.3 185 46-234 145-333 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 1.7E-34 3.8E-39 233.7 10.7 190 43-234 180-396 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 8.5E-29 1.8E-33 213.0 6.6 225 3-234 22-256 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.5E-25 3.3E-30 176.2 6.9 182 44-233 218-426 (446)
5 smart00647 IBR In Between Ring 99.3 1.8E-12 3.8E-17 82.0 5.2 63 118-180 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 1.1E-12 2.4E-17 82.9 0.9 63 118-180 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.9 4.6E-10 1E-14 64.2 0.7 40 50-95 1-40 (42)
8 PF00097 zf-C3HC4: Zinc finger 98.8 7E-09 1.5E-13 59.2 3.2 39 50-95 1-39 (41)
9 PF13923 zf-C3HC4_2: Zinc fing 98.7 5.1E-09 1.1E-13 59.0 2.0 37 50-95 1-37 (39)
10 PF13639 zf-RING_2: Ring finge 98.7 2.9E-09 6.3E-14 61.8 1.0 40 49-95 2-41 (44)
11 KOG0320 Predicted E3 ubiquitin 98.7 1.4E-08 3E-13 74.7 4.7 58 43-110 127-184 (187)
12 PF14634 zf-RING_5: zinc-RING 98.7 2.2E-08 4.8E-13 58.0 3.9 43 49-100 1-43 (44)
13 PF13445 zf-RING_UBOX: RING-ty 98.7 1.3E-08 2.9E-13 58.1 2.4 43 50-95 1-43 (43)
14 PLN03208 E3 ubiquitin-protein 98.6 3.6E-08 7.8E-13 74.4 4.2 64 45-113 16-88 (193)
15 cd00162 RING RING-finger (Real 98.5 1.8E-07 3.9E-12 54.1 3.9 44 49-102 1-44 (45)
16 PF13920 zf-C3HC4_3: Zinc fing 98.4 2.3E-07 5.1E-12 55.2 2.8 46 47-104 2-48 (50)
17 KOG2177 Predicted E3 ubiquitin 98.2 2.7E-06 5.9E-11 70.4 5.4 111 44-182 10-124 (386)
18 KOG0317 Predicted E3 ubiquitin 98.2 1E-06 2.2E-11 69.9 2.6 52 45-108 237-288 (293)
19 smart00184 RING Ring finger. E 98.2 2.7E-06 5.9E-11 47.2 3.7 37 50-95 1-37 (39)
20 PHA02926 zinc finger-like prot 98.2 2.8E-06 6E-11 65.1 4.7 58 44-104 167-230 (242)
21 smart00504 Ubox Modified RING 98.1 4.4E-06 9.5E-11 52.2 4.0 51 48-110 2-52 (63)
22 KOG0823 Predicted E3 ubiquitin 98.1 3E-06 6.5E-11 65.3 3.4 59 45-112 45-103 (230)
23 KOG2164 Predicted E3 ubiquitin 98.1 2.3E-06 5.1E-11 73.0 3.0 59 47-112 186-244 (513)
24 PHA02929 N1R/p28-like protein; 98.1 4.3E-06 9.2E-11 65.9 4.2 51 45-104 172-227 (238)
25 TIGR00599 rad18 DNA repair pro 98.1 3.9E-06 8.5E-11 70.9 4.1 68 44-123 23-91 (397)
26 KOG0287 Postreplication repair 98.0 3.1E-06 6.7E-11 68.5 2.3 66 44-121 20-86 (442)
27 TIGR00570 cdk7 CDK-activating 97.9 5.2E-05 1.1E-09 61.7 6.9 56 47-110 3-60 (309)
28 COG5540 RING-finger-containing 97.7 3.7E-05 8E-10 61.5 3.6 54 44-105 320-373 (374)
29 PF14835 zf-RING_6: zf-RING of 97.5 7.2E-06 1.6E-10 50.2 -2.1 51 44-107 4-54 (65)
30 KOG4628 Predicted E3 ubiquitin 97.5 8.1E-05 1.7E-09 61.6 3.0 46 48-101 230-275 (348)
31 PF11789 zf-Nse: Zinc-finger o 97.4 0.00012 2.6E-09 44.6 2.3 47 47-100 11-57 (57)
32 COG5574 PEX10 RING-finger-cont 97.3 0.00024 5.2E-09 56.0 3.9 54 45-108 213-266 (271)
33 PF12678 zf-rbx1: RING-H2 zinc 97.3 0.00012 2.7E-09 47.1 1.8 40 49-95 21-70 (73)
34 KOG0978 E3 ubiquitin ligase in 97.2 0.00014 3.1E-09 65.2 1.8 57 44-111 640-696 (698)
35 smart00647 IBR In Between Ring 97.2 0.00054 1.2E-08 42.7 3.9 30 205-234 16-50 (64)
36 KOG1002 Nucleotide excision re 97.1 0.00031 6.8E-09 60.4 2.1 56 44-106 533-588 (791)
37 COG5432 RAD18 RING-finger-cont 97.0 0.00043 9.3E-09 55.2 2.4 67 44-122 22-89 (391)
38 PF11793 FANCL_C: FANCL C-term 97.0 0.00032 7E-09 44.7 1.3 57 47-105 2-67 (70)
39 PF04564 U-box: U-box domain; 97.0 0.00039 8.5E-09 44.8 1.7 51 46-107 3-53 (73)
40 KOG2879 Predicted E3 ubiquitin 96.7 0.0021 4.5E-08 51.1 3.7 51 45-104 237-287 (298)
41 PF01485 IBR: IBR domain; Int 96.6 0.00073 1.6E-08 42.1 0.4 31 204-234 15-50 (64)
42 COG5243 HRD1 HRD ubiquitin lig 96.3 0.004 8.6E-08 51.6 3.5 53 45-106 285-347 (491)
43 KOG1039 Predicted E3 ubiquitin 96.3 0.0033 7.2E-08 52.4 3.1 57 45-103 159-220 (344)
44 PF10571 UPF0547: Uncharacteri 96.2 0.0023 4.9E-08 32.2 1.0 23 208-234 1-24 (26)
45 KOG2660 Locus-specific chromos 96.0 0.0035 7.6E-08 51.1 1.8 51 44-105 12-62 (331)
46 smart00744 RINGv The RING-vari 95.8 0.024 5.1E-07 33.3 4.1 41 49-95 1-46 (49)
47 KOG4367 Predicted Zn-finger pr 95.7 0.0083 1.8E-07 50.8 2.7 35 45-82 2-36 (699)
48 KOG4185 Predicted E3 ubiquitin 95.5 0.036 7.9E-07 45.7 5.8 122 47-177 3-130 (296)
49 smart00661 RPOL9 RNA polymeras 95.3 0.012 2.5E-07 35.0 1.8 27 208-234 1-30 (52)
50 KOG0828 Predicted E3 ubiquitin 95.3 0.014 3E-07 50.3 2.7 53 44-104 568-634 (636)
51 KOG0802 E3 ubiquitin ligase [P 95.2 0.016 3.5E-07 51.9 3.2 48 45-101 289-338 (543)
52 KOG1812 Predicted E3 ubiquitin 95.2 0.004 8.8E-08 53.1 -0.6 105 46-179 237-346 (384)
53 PF14570 zf-RING_4: RING/Ubox 95.2 0.023 4.9E-07 33.0 2.6 46 50-103 1-47 (48)
54 PF12861 zf-Apc11: Anaphase-pr 95.2 0.027 5.9E-07 36.9 3.2 52 47-104 21-82 (85)
55 KOG0311 Predicted E3 ubiquitin 95.2 0.0028 6.1E-08 52.1 -1.7 52 42-103 38-89 (381)
56 KOG0006 E3 ubiquitin-protein l 95.1 0.029 6.4E-07 45.6 4.0 94 67-175 341-436 (446)
57 PHA00626 hypothetical protein 95.1 0.017 3.8E-07 34.2 2.0 26 209-234 2-33 (59)
58 KOG4265 Predicted E3 ubiquitin 95.1 0.027 5.8E-07 46.7 3.8 49 44-104 287-336 (349)
59 KOG1814 Predicted E3 ubiquitin 94.8 0.049 1.1E-06 45.9 4.7 112 45-174 271-404 (445)
60 KOG1428 Inhibitor of type V ad 94.8 0.044 9.5E-07 53.2 4.6 69 44-114 3483-3554(3738)
61 KOG0297 TNF receptor-associate 94.7 0.034 7.5E-07 47.7 3.7 52 44-106 18-69 (391)
62 KOG4159 Predicted E3 ubiquitin 94.6 0.036 7.8E-07 47.3 3.5 49 44-104 81-129 (398)
63 KOG0824 Predicted E3 ubiquitin 94.5 0.022 4.8E-07 46.0 1.9 52 47-109 7-58 (324)
64 COG5152 Uncharacterized conser 94.4 0.022 4.8E-07 43.1 1.5 33 46-81 195-227 (259)
65 KOG2817 Predicted E3 ubiquitin 94.2 0.049 1.1E-06 45.8 3.4 61 44-110 331-391 (394)
66 KOG4739 Uncharacterized protei 94.1 0.018 3.8E-07 45.2 0.6 49 47-107 3-51 (233)
67 PF05883 Baculo_RING: Baculovi 94.1 0.033 7.1E-07 39.8 1.8 37 46-82 25-67 (134)
68 PRK00432 30S ribosomal protein 93.9 0.034 7.3E-07 32.8 1.3 27 206-234 19-47 (50)
69 PF02150 RNA_POL_M_15KD: RNA p 93.8 0.044 9.4E-07 29.7 1.6 27 208-234 2-30 (35)
70 KOG1645 RING-finger-containing 93.8 0.098 2.1E-06 44.1 4.3 56 46-108 3-60 (463)
71 PF13719 zinc_ribbon_5: zinc-r 93.6 0.05 1.1E-06 29.9 1.7 31 134-166 2-35 (37)
72 KOG1952 Transcription factor N 93.5 0.091 2E-06 48.3 3.9 55 44-100 188-243 (950)
73 KOG1734 Predicted RING-contain 93.1 0.025 5.4E-07 44.9 -0.1 56 47-109 224-286 (328)
74 KOG4692 Predicted E3 ubiquitin 93.0 0.052 1.1E-06 44.9 1.6 35 45-82 420-454 (489)
75 KOG3039 Uncharacterized conser 92.9 0.12 2.6E-06 40.6 3.4 57 45-110 219-276 (303)
76 KOG1785 Tyrosine kinase negati 92.3 0.083 1.8E-06 44.4 1.8 47 46-100 368-414 (563)
77 COG5220 TFB3 Cdk activating ki 91.9 0.055 1.2E-06 42.3 0.4 52 47-104 10-64 (314)
78 PF13717 zinc_ribbon_4: zinc-r 91.9 0.13 2.8E-06 28.0 1.8 31 134-166 2-35 (36)
79 KOG0827 Predicted E3 ubiquitin 91.7 0.16 3.5E-06 42.6 2.8 48 47-100 4-52 (465)
80 KOG4445 Uncharacterized conser 91.7 0.17 3.7E-06 41.0 2.9 40 45-84 113-152 (368)
81 KOG0804 Cytoplasmic Zn-finger 91.5 0.082 1.8E-06 45.1 1.0 49 45-104 173-222 (493)
82 COG5222 Uncharacterized conser 91.4 0.24 5.2E-06 40.1 3.5 44 48-101 275-318 (427)
83 PF14952 zf-tcix: Putative tre 91.4 0.1 2.2E-06 29.4 1.0 27 204-234 8-37 (44)
84 KOG4172 Predicted E3 ubiquitin 91.3 0.069 1.5E-06 31.6 0.3 44 48-102 8-52 (62)
85 PRK00398 rpoP DNA-directed RNA 90.8 0.25 5.3E-06 28.5 2.3 26 208-233 4-30 (46)
86 PF07975 C1_4: TFIIH C1-like d 90.5 0.071 1.5E-06 31.4 -0.2 37 141-177 4-42 (51)
87 PF04641 Rtf2: Rtf2 RING-finge 90.4 0.37 7.9E-06 39.1 3.8 71 44-124 110-182 (260)
88 PF14447 Prok-RING_4: Prokaryo 89.9 0.092 2E-06 31.3 -0.0 47 46-106 6-52 (55)
89 PF10367 Vps39_2: Vacuolar sor 89.9 0.12 2.5E-06 35.6 0.5 34 44-78 75-108 (109)
90 KOG3800 Predicted E3 ubiquitin 89.7 0.75 1.6E-05 37.2 4.9 51 49-107 2-54 (300)
91 CHL00174 accD acetyl-CoA carbo 89.4 0.096 2.1E-06 42.9 -0.3 30 205-234 36-67 (296)
92 PF14569 zf-UDP: Zinc-binding 89.3 0.43 9.3E-06 30.5 2.6 57 141-226 14-70 (80)
93 PF09297 zf-NADH-PPase: NADH p 89.2 0.35 7.7E-06 25.4 1.9 27 207-233 3-30 (32)
94 smart00661 RPOL9 RNA polymeras 89.2 0.32 6.9E-06 28.7 2.0 28 136-165 2-29 (52)
95 KOG1815 Predicted E3 ubiquitin 89.2 0.36 7.9E-06 42.3 3.1 40 133-176 225-268 (444)
96 KOG1001 Helicase-like transcri 89.1 0.23 4.9E-06 45.6 1.8 52 48-110 455-506 (674)
97 PF02150 RNA_POL_M_15KD: RNA p 88.7 0.17 3.6E-06 27.4 0.4 28 135-165 2-29 (35)
98 PHA03096 p28-like protein; Pro 88.7 0.3 6.6E-06 39.9 2.1 39 48-86 179-222 (284)
99 COG1998 RPS31 Ribosomal protei 88.5 0.32 6.8E-06 28.2 1.5 29 205-233 17-46 (51)
100 PF14803 Nudix_N_2: Nudix N-te 88.1 0.4 8.6E-06 25.7 1.6 25 208-232 1-30 (34)
101 KOG2034 Vacuolar sorting prote 87.1 0.42 9E-06 44.5 2.2 41 44-85 814-854 (911)
102 KOG3579 Predicted E3 ubiquitin 86.8 0.48 1E-05 38.2 2.1 54 45-100 266-321 (352)
103 TIGR02098 MJ0042_CXXC MJ0042 f 86.8 0.37 8.1E-06 26.4 1.1 30 135-166 3-35 (38)
104 PF13240 zinc_ribbon_2: zinc-r 86.2 0.41 8.9E-06 23.2 1.0 22 136-165 1-22 (23)
105 PLN03086 PRLI-interacting fact 86.1 1.4 3E-05 39.6 4.9 59 89-166 405-463 (567)
106 PF06677 Auto_anti-p27: Sjogre 86.1 0.79 1.7E-05 25.7 2.2 23 207-231 17-41 (41)
107 COG5175 MOT2 Transcriptional r 85.9 1.4 3.1E-05 36.5 4.4 55 47-109 14-69 (480)
108 KOG1941 Acetylcholine receptor 85.3 0.37 8.1E-06 40.6 0.9 50 45-101 363-413 (518)
109 KOG3002 Zn finger protein [Gen 84.6 0.74 1.6E-05 38.0 2.3 46 45-104 46-91 (299)
110 PF03119 DNA_ligase_ZBD: NAD-d 84.3 1.2 2.5E-05 22.7 2.1 21 209-229 1-21 (28)
111 PRK08665 ribonucleotide-diphos 84.1 0.62 1.3E-05 43.6 1.8 24 208-233 725-749 (752)
112 PF12773 DZR: Double zinc ribb 84.0 0.9 2E-05 26.5 2.0 26 134-164 12-37 (50)
113 COG1645 Uncharacterized Zn-fin 84.0 0.65 1.4E-05 33.1 1.5 26 206-233 27-53 (131)
114 PF01599 Ribosomal_S27: Riboso 83.7 0.97 2.1E-05 26.1 1.9 27 206-232 17-46 (47)
115 KOG2807 RNA polymerase II tran 83.7 0.15 3.3E-06 41.7 -1.9 82 71-175 277-364 (378)
116 PF13248 zf-ribbon_3: zinc-rib 83.6 0.62 1.3E-05 23.2 1.0 23 135-165 3-25 (26)
117 KOG1813 Predicted E3 ubiquitin 83.6 0.36 7.8E-06 39.1 0.1 33 47-82 241-273 (313)
118 PRK14714 DNA polymerase II lar 83.5 1.2 2.6E-05 43.3 3.5 29 135-173 668-701 (1337)
119 PF14446 Prok-RING_1: Prokaryo 82.9 1.6 3.5E-05 26.0 2.7 33 47-79 5-38 (54)
120 COG2888 Predicted Zn-ribbon RN 82.6 1.4 3E-05 26.7 2.3 32 136-171 11-42 (61)
121 PRK14559 putative protein seri 82.6 0.86 1.9E-05 41.8 2.1 14 205-218 39-52 (645)
122 KOG1940 Zn-finger protein [Gen 82.5 0.98 2.1E-05 36.7 2.2 46 47-101 158-204 (276)
123 COG1997 RPL43A Ribosomal prote 81.5 2.4 5.2E-05 27.9 3.3 31 204-234 32-63 (89)
124 TIGR03655 anti_R_Lar restricti 81.2 1.4 3.1E-05 26.1 2.1 27 207-233 1-35 (53)
125 PF12906 RINGv: RING-variant d 81.1 1.1 2.3E-05 26.0 1.5 33 50-83 1-38 (47)
126 PF08271 TF_Zn_Ribbon: TFIIB z 80.3 1.9 4E-05 24.3 2.3 24 209-232 2-27 (43)
127 PRK14890 putative Zn-ribbon RN 80.0 2.3 5E-05 25.8 2.6 31 136-170 9-39 (59)
128 PF08746 zf-RING-like: RING-li 79.6 1.2 2.7E-05 25.2 1.4 41 50-95 1-41 (43)
129 COG5219 Uncharacterized conser 79.4 0.78 1.7E-05 43.2 0.7 57 41-104 1463-1523(1525)
130 PRK00420 hypothetical protein; 79.1 1.6 3.5E-05 30.4 2.0 25 206-232 22-48 (112)
131 COG1198 PriA Primosomal protei 78.8 5 0.00011 37.4 5.7 10 207-216 475-484 (730)
132 PF07191 zinc-ribbons_6: zinc- 78.8 1.2 2.6E-05 28.1 1.2 24 209-234 3-27 (70)
133 TIGR00622 ssl1 transcription f 78.1 2 4.2E-05 29.9 2.2 41 135-177 56-102 (112)
134 KOG3970 Predicted E3 ubiquitin 77.3 3 6.4E-05 32.6 3.2 54 47-103 50-104 (299)
135 PRK04023 DNA polymerase II lar 76.4 2.2 4.8E-05 40.7 2.7 29 135-173 627-660 (1121)
136 PF02891 zf-MIZ: MIZ/SP-RING z 76.3 2.7 5.8E-05 24.6 2.2 47 48-101 3-49 (50)
137 KOG0801 Predicted E3 ubiquitin 76.0 0.95 2.1E-05 33.4 0.2 29 45-73 175-203 (205)
138 PF07282 OrfB_Zn_ribbon: Putat 76.0 1.5 3.2E-05 27.5 1.1 28 206-233 27-55 (69)
139 TIGR01206 lysW lysine biosynth 75.9 2.8 6E-05 25.1 2.2 30 135-166 3-32 (54)
140 PF05605 zf-Di19: Drought indu 75.7 2.4 5.2E-05 25.2 1.9 40 47-103 2-41 (54)
141 KOG0825 PHD Zn-finger protein 75.5 0.77 1.7E-05 42.3 -0.4 42 45-86 94-139 (1134)
142 PF08792 A2L_zn_ribbon: A2L zi 75.0 3.2 6.9E-05 22.0 2.0 28 207-234 3-31 (33)
143 TIGR02443 conserved hypothetic 74.5 3.4 7.5E-05 25.0 2.3 26 208-233 10-40 (59)
144 PLN02638 cellulose synthase A 74.2 2.5 5.3E-05 40.7 2.5 60 136-226 19-78 (1079)
145 PRK14873 primosome assembly pr 73.6 7.6 0.00016 36.0 5.4 18 155-172 382-400 (665)
146 TIGR00570 cdk7 CDK-activating 72.7 2.3 4.9E-05 35.2 1.7 53 136-221 5-57 (309)
147 KOG2906 RNA polymerase III sub 71.5 2.6 5.6E-05 28.3 1.4 29 135-165 2-30 (105)
148 COG1594 RPB9 DNA-directed RNA 71.2 2.7 5.8E-05 29.4 1.6 30 135-166 3-32 (113)
149 PRK14892 putative transcriptio 71.1 3.9 8.5E-05 27.8 2.3 30 205-234 19-52 (99)
150 KOG0320 Predicted E3 ubiquitin 70.7 0.94 2E-05 34.0 -0.9 31 160-219 149-179 (187)
151 PF06844 DUF1244: Protein of u 70.6 4.5 9.8E-05 25.1 2.2 17 72-88 12-28 (68)
152 COG5109 Uncharacterized conser 70.6 4.3 9.3E-05 33.4 2.7 58 44-107 333-390 (396)
153 PRK00420 hypothetical protein; 70.5 12 0.00025 26.1 4.5 26 135-165 24-49 (112)
154 PF09788 Tmemb_55A: Transmembr 70.1 6.5 0.00014 31.4 3.6 21 131-151 120-140 (256)
155 PF09526 DUF2387: Probable met 69.8 4.4 9.4E-05 25.8 2.1 26 208-233 9-39 (71)
156 PLN02189 cellulose synthase 69.8 3.9 8.4E-05 39.3 2.7 60 136-226 36-95 (1040)
157 PHA02825 LAP/PHD finger-like p 68.7 8.5 0.00018 28.5 3.7 51 45-106 6-61 (162)
158 PF14354 Lar_restr_allev: Rest 68.6 5.3 0.00011 24.2 2.3 27 206-232 2-37 (61)
159 PRK09710 lar restriction allev 68.1 5.3 0.00012 24.7 2.2 28 205-232 4-35 (64)
160 COG5236 Uncharacterized conser 67.4 11 0.00024 31.5 4.6 33 45-80 59-91 (493)
161 PF14149 YhfH: YhfH-like prote 67.2 0.64 1.4E-05 25.3 -1.7 28 201-228 7-34 (37)
162 PF06827 zf-FPG_IleRS: Zinc fi 67.1 3.1 6.7E-05 21.3 0.9 24 208-231 2-28 (30)
163 cd00021 BBOX B-Box-type zinc f 66.8 2.8 6.2E-05 22.6 0.8 25 155-179 11-35 (39)
164 PRK08115 ribonucleotide-diphos 66.1 2.9 6.3E-05 39.5 1.1 24 208-233 828-853 (858)
165 PF14471 DUF4428: Domain of un 65.4 6.6 0.00014 23.1 2.2 30 49-80 1-30 (51)
166 KOG3039 Uncharacterized conser 65.2 6.3 0.00014 31.4 2.6 40 44-86 40-79 (303)
167 PF00643 zf-B_box: B-box zinc 64.8 1 2.2E-05 25.1 -1.4 25 155-179 14-38 (42)
168 PF09538 FYDLN_acid: Protein o 64.8 4.6 0.0001 28.0 1.6 28 134-166 9-36 (108)
169 smart00659 RPOLCX RNA polymera 63.5 7.8 0.00017 22.0 2.2 13 206-218 18-30 (44)
170 TIGR00373 conserved hypothetic 63.3 7.2 0.00016 29.0 2.6 31 132-165 107-137 (158)
171 PF14369 zf-RING_3: zinc-finge 63.0 9.2 0.0002 20.5 2.3 30 134-166 2-31 (35)
172 PF10497 zf-4CXXC_R1: Zinc-fin 62.9 16 0.00034 25.2 4.0 54 47-102 7-70 (105)
173 KOG0823 Predicted E3 ubiquitin 62.2 2.7 5.9E-05 33.0 0.2 37 155-219 60-96 (230)
174 PF05129 Elf1: Transcription e 62.1 3.1 6.7E-05 27.2 0.4 29 206-234 21-56 (81)
175 PF14445 Prok-RING_2: Prokaryo 62.1 1.7 3.7E-05 25.3 -0.7 35 47-81 7-41 (57)
176 PF13453 zf-TFIIB: Transcripti 61.8 3.9 8.5E-05 22.7 0.7 27 136-164 1-27 (41)
177 PF03604 DNA_RNApol_7kD: DNA d 61.6 6.6 0.00014 20.7 1.5 23 141-166 5-27 (32)
178 KOG4684 Uncharacterized conser 61.4 9 0.00019 29.8 2.8 19 131-149 135-153 (275)
179 PHA02929 N1R/p28-like protein; 61.0 4.6 0.0001 32.2 1.3 39 134-174 174-212 (238)
180 PRK12286 rpmF 50S ribosomal pr 59.9 6.6 0.00014 23.8 1.5 24 204-232 24-48 (57)
181 PF01873 eIF-5_eIF-2B: Domain 59.6 17 0.00037 25.9 3.8 37 195-233 83-123 (125)
182 smart00336 BBOX B-Box-type zin 59.2 5.9 0.00013 21.7 1.2 24 155-178 14-37 (42)
183 KOG0826 Predicted E3 ubiquitin 59.0 8.1 0.00017 32.1 2.3 48 45-101 298-345 (357)
184 smart00249 PHD PHD zinc finger 58.7 5.3 0.00012 22.1 1.0 33 49-81 1-33 (47)
185 PF01428 zf-AN1: AN1-like Zinc 58.6 5.3 0.00012 22.5 0.9 17 157-173 14-30 (43)
186 PHA02862 5L protein; Provision 58.4 15 0.00032 26.8 3.3 47 48-105 3-54 (156)
187 PF05290 Baculo_IE-1: Baculovi 58.2 16 0.00035 26.2 3.4 53 45-103 78-131 (140)
188 PLN02400 cellulose synthase 57.1 6.8 0.00015 37.9 1.9 60 136-226 38-97 (1085)
189 KOG3053 Uncharacterized conser 57.0 12 0.00026 30.0 2.9 56 45-102 18-80 (293)
190 smart00834 CxxC_CXXC_SSSS Puta 56.9 8.7 0.00019 21.0 1.6 29 135-165 6-35 (41)
191 PRK05978 hypothetical protein; 56.4 7.1 0.00015 28.7 1.5 28 207-234 33-62 (148)
192 PLN02436 cellulose synthase A 56.1 9.8 0.00021 36.9 2.7 60 136-226 38-97 (1094)
193 PRK14714 DNA polymerase II lar 55.3 9.8 0.00021 37.5 2.6 18 157-174 668-689 (1337)
194 COG1579 Zn-ribbon protein, pos 55.1 8.8 0.00019 30.6 1.9 58 106-165 166-230 (239)
195 TIGR00686 phnA alkylphosphonat 55.0 7.7 0.00017 26.7 1.4 26 136-166 4-29 (109)
196 KOG2114 Vacuolar assembly/sort 55.0 9.4 0.0002 35.8 2.3 40 48-101 841-880 (933)
197 KOG0978 E3 ubiquitin ligase in 54.5 3.5 7.6E-05 37.9 -0.4 30 160-217 659-688 (698)
198 PF02591 DUF164: Putative zinc 54.5 13 0.00028 22.2 2.2 19 198-216 37-55 (56)
199 COG1645 Uncharacterized Zn-fin 54.4 7.7 0.00017 27.8 1.4 24 135-164 29-52 (131)
200 PRK06266 transcription initiat 53.9 14 0.00031 28.0 2.9 59 103-165 85-145 (178)
201 PRK11827 hypothetical protein; 53.6 13 0.00027 22.8 2.0 28 207-234 8-36 (60)
202 PF06906 DUF1272: Protein of u 53.5 25 0.00054 21.1 3.1 46 48-104 6-52 (57)
203 KOG1493 Anaphase-promoting com 53.2 7.5 0.00016 24.9 1.0 48 49-102 22-79 (84)
204 PLN02915 cellulose synthase A 53.1 11 0.00024 36.4 2.5 57 141-226 20-76 (1044)
205 PF08274 PhnA_Zn_Ribbon: PhnA 53.1 5.9 0.00013 20.5 0.5 26 136-166 4-29 (30)
206 COG2051 RPS27A Ribosomal prote 52.6 11 0.00023 23.5 1.6 31 135-168 20-50 (67)
207 PF12760 Zn_Tnp_IS1595: Transp 52.3 41 0.00088 19.1 4.0 26 208-233 19-46 (46)
208 PF00098 zf-CCHC: Zinc knuckle 52.3 8.5 0.00018 17.2 0.9 16 166-181 2-17 (18)
209 PRK14559 putative protein seri 51.7 13 0.00028 34.4 2.6 31 133-173 14-50 (645)
210 smart00734 ZnF_Rad18 Rad18-lik 51.4 8.2 0.00018 19.2 0.8 20 92-113 2-21 (26)
211 COG3492 Uncharacterized protei 51.3 18 0.00038 24.0 2.5 17 71-87 42-58 (104)
212 KOG3268 Predicted E3 ubiquitin 51.2 20 0.00043 27.1 3.1 59 45-105 163-229 (234)
213 PRK10220 hypothetical protein; 50.8 11 0.00024 26.0 1.6 26 136-166 5-30 (111)
214 COG3813 Uncharacterized protei 50.6 15 0.00033 23.2 2.0 46 49-106 7-54 (84)
215 smart00531 TFIIE Transcription 50.5 15 0.00032 27.0 2.4 32 132-165 97-132 (147)
216 COG5151 SSL1 RNA polymerase II 49.9 4.1 8.9E-05 33.5 -0.7 75 90-175 321-407 (421)
217 PF07503 zf-HYPF: HypF finger; 49.6 6.6 0.00014 21.1 0.3 31 72-104 1-32 (35)
218 KOG4275 Predicted E3 ubiquitin 49.4 6.3 0.00014 32.2 0.3 31 47-80 300-331 (350)
219 PF07754 DUF1610: Domain of un 49.3 8.2 0.00018 18.9 0.6 8 207-214 16-23 (24)
220 cd00065 FYVE FYVE domain; Zinc 49.2 12 0.00027 22.1 1.5 36 48-83 3-39 (57)
221 PLN03086 PRLI-interacting fact 47.9 14 0.00029 33.5 2.1 30 205-234 431-463 (567)
222 KOG3161 Predicted E3 ubiquitin 47.5 7.4 0.00016 35.4 0.5 36 47-82 11-47 (861)
223 KOG2932 E3 ubiquitin ligase in 47.4 11 0.00023 31.2 1.3 32 47-80 90-121 (389)
224 KOG2164 Predicted E3 ubiquitin 46.6 8.2 0.00018 34.0 0.6 35 161-219 203-237 (513)
225 KOG4362 Transcriptional regula 45.6 4.2 9.1E-05 37.3 -1.3 59 43-110 17-75 (684)
226 PF14205 Cys_rich_KTR: Cystein 45.6 21 0.00045 21.3 2.0 31 133-165 3-37 (55)
227 PRK01103 formamidopyrimidine/5 45.4 19 0.00042 29.3 2.6 26 207-232 245-273 (274)
228 PRK03824 hypA hydrogenase nick 45.3 28 0.00061 25.1 3.1 14 134-149 70-83 (135)
229 PRK09521 exosome complex RNA-b 45.2 18 0.00038 27.7 2.2 25 208-233 150-175 (189)
230 COG5194 APC11 Component of SCF 45.0 29 0.00064 22.5 2.8 18 66-83 52-69 (88)
231 PLN02195 cellulose synthase A 45.0 17 0.00037 35.0 2.4 30 141-171 11-40 (977)
232 PRK14811 formamidopyrimidine-D 44.9 23 0.00049 28.9 2.9 28 206-233 234-264 (269)
233 KOG2923 Uncharacterized conser 44.8 18 0.00039 22.3 1.7 21 199-219 36-56 (67)
234 TIGR02300 FYDLN_acid conserved 44.5 17 0.00036 25.9 1.7 28 134-166 9-36 (129)
235 PF05715 zf-piccolo: Piccolo Z 43.9 12 0.00027 22.7 0.9 37 136-174 4-40 (61)
236 KOG2979 Protein involved in DN 43.8 33 0.00072 27.6 3.5 48 47-101 176-223 (262)
237 KOG1100 Predicted E3 ubiquitin 43.6 16 0.00034 28.6 1.7 25 50-77 161-186 (207)
238 TIGR01053 LSD1 zinc finger dom 43.5 29 0.00062 18.1 2.2 24 209-232 3-27 (31)
239 KOG0825 PHD Zn-finger protein 43.4 33 0.00071 32.3 3.8 50 47-105 123-172 (1134)
240 COG0266 Nei Formamidopyrimidin 43.1 24 0.00051 28.8 2.7 27 206-232 244-273 (273)
241 COG3357 Predicted transcriptio 42.8 67 0.0015 21.4 4.2 59 102-165 18-85 (97)
242 smart00064 FYVE Protein presen 42.4 20 0.00043 22.1 1.8 37 47-83 10-47 (68)
243 PF04981 NMD3: NMD3 family ; 42.2 14 0.0003 29.5 1.2 15 205-219 33-47 (236)
244 COG2260 Predicted Zn-ribbon RN 42.1 17 0.00037 22.0 1.3 14 206-219 4-17 (59)
245 PF09889 DUF2116: Uncharacteri 42.1 11 0.00025 22.9 0.6 13 208-220 4-16 (59)
246 PRK00415 rps27e 30S ribosomal 41.9 21 0.00045 21.8 1.6 31 135-168 12-42 (59)
247 PF14353 CpXC: CpXC protein 41.5 13 0.00029 26.3 1.0 45 92-148 2-50 (128)
248 KOG2930 SCF ubiquitin ligase, 41.4 21 0.00046 24.3 1.8 23 66-95 79-101 (114)
249 PF02318 FYVE_2: FYVE-type zin 41.4 57 0.0012 22.8 4.1 36 133-173 53-88 (118)
250 COG4847 Uncharacterized protei 41.1 18 0.00039 24.2 1.4 40 46-86 5-44 (103)
251 PRK10445 endonuclease VIII; Pr 40.8 24 0.00052 28.6 2.5 25 207-231 235-262 (263)
252 PLN00209 ribosomal protein S27 40.6 19 0.0004 23.7 1.4 31 135-168 37-67 (86)
253 PF01396 zf-C4_Topoisom: Topoi 40.4 19 0.0004 19.8 1.2 20 208-228 2-24 (39)
254 PTZ00083 40S ribosomal protein 40.3 19 0.00041 23.6 1.4 31 135-168 36-66 (85)
255 COG5216 Uncharacterized conser 40.1 18 0.00039 21.8 1.2 20 198-217 35-54 (67)
256 TIGR01384 TFS_arch transcripti 40.1 18 0.00039 24.6 1.4 24 136-165 2-25 (104)
257 COG1198 PriA Primosomal protei 39.8 36 0.00078 32.0 3.6 34 136-173 446-484 (730)
258 PF10426 zf-RAG1: Recombinatio 39.7 3.8 8.3E-05 21.1 -1.5 20 91-110 2-21 (30)
259 PF01780 Ribosomal_L37ae: Ribo 39.4 12 0.00026 24.9 0.4 30 205-234 33-63 (90)
260 PF06943 zf-LSD1: LSD1 zinc fi 39.3 44 0.00095 16.5 2.3 23 210-232 1-24 (25)
261 TIGR00577 fpg formamidopyrimid 38.9 26 0.00056 28.6 2.4 25 207-231 245-272 (272)
262 PRK14810 formamidopyrimidine-D 38.8 30 0.00066 28.2 2.8 26 206-231 243-271 (272)
263 PF03884 DUF329: Domain of unk 38.6 16 0.00035 22.1 0.9 16 207-222 2-17 (57)
264 smart00653 eIF2B_5 domain pres 38.4 48 0.001 23.0 3.3 29 205-233 78-110 (110)
265 TIGR00311 aIF-2beta translatio 38.1 49 0.0011 23.9 3.4 29 205-233 95-127 (133)
266 PF00628 PHD: PHD-finger; Int 38.0 12 0.00027 21.5 0.3 34 49-82 1-34 (51)
267 PF03833 PolC_DP2: DNA polymer 37.6 11 0.00024 35.5 0.0 16 157-172 668-688 (900)
268 PF08209 Sgf11: Sgf11 (transcr 37.2 19 0.0004 19.1 0.8 13 207-219 4-16 (33)
269 PF05191 ADK_lid: Adenylate ki 37.1 35 0.00075 18.4 1.9 28 136-165 3-30 (36)
270 PF01667 Ribosomal_S27e: Ribos 37.0 28 0.0006 20.9 1.7 31 135-168 8-38 (55)
271 KOG0309 Conserved WD40 repeat- 36.6 28 0.00061 32.5 2.4 39 44-83 1025-1063(1081)
272 PF09943 DUF2175: Uncharacteri 36.6 33 0.00071 23.4 2.1 40 47-87 2-41 (101)
273 COG1096 Predicted RNA-binding 36.6 28 0.0006 26.6 2.0 23 208-232 150-173 (188)
274 cd00350 rubredoxin_like Rubred 36.6 34 0.00073 17.9 1.8 23 136-164 3-25 (33)
275 PRK13945 formamidopyrimidine-D 36.5 30 0.00065 28.4 2.4 25 207-231 254-281 (282)
276 PRK03988 translation initiatio 35.8 54 0.0012 23.8 3.3 29 205-233 100-132 (138)
277 PF11023 DUF2614: Protein of u 35.7 22 0.00049 24.6 1.3 11 166-176 87-97 (114)
278 KOG2691 RNA polymerase II subu 35.5 19 0.0004 24.8 0.8 31 133-165 3-35 (113)
279 PRK12495 hypothetical protein; 35.4 61 0.0013 25.5 3.7 25 135-165 43-67 (226)
280 PF10764 Gin: Inhibitor of sig 35.1 21 0.00046 20.5 0.9 35 49-87 1-35 (46)
281 PRK00241 nudC NADH pyrophospha 35.1 28 0.0006 28.2 2.0 29 205-233 97-126 (256)
282 PRK13264 3-hydroxyanthranilate 34.8 17 0.00036 27.6 0.6 24 196-219 146-169 (177)
283 TIGR01031 rpmF_bact ribosomal 34.7 30 0.00064 20.7 1.6 23 205-232 24-47 (55)
284 TIGR00100 hypA hydrogenase nic 34.5 36 0.00078 23.8 2.2 25 134-164 70-94 (115)
285 COG3024 Uncharacterized protei 34.4 21 0.00046 22.0 0.9 16 205-220 5-20 (65)
286 PRK12336 translation initiatio 34.2 54 0.0012 25.5 3.3 29 205-233 96-128 (201)
287 PF03854 zf-P11: P-11 zinc fin 34.1 9.4 0.0002 22.1 -0.6 43 48-104 3-46 (50)
288 KOG2807 RNA polymerase II tran 33.9 18 0.00038 30.2 0.6 30 48-77 331-360 (378)
289 PF13913 zf-C2HC_2: zinc-finge 33.8 22 0.00047 17.3 0.7 18 92-111 3-20 (25)
290 TIGR00595 priA primosomal prot 33.7 32 0.0007 30.8 2.3 26 208-233 223-249 (505)
291 cd02335 ZZ_ADA2 Zinc finger, Z 33.6 52 0.0011 18.9 2.5 32 49-80 2-34 (49)
292 TIGR03037 anthran_nbaC 3-hydro 33.6 19 0.0004 26.9 0.7 19 197-215 141-159 (159)
293 PRK12380 hydrogenase nickel in 33.5 37 0.00081 23.6 2.2 25 134-164 70-94 (113)
294 PF06467 zf-FCS: MYM-type Zinc 33.5 34 0.00074 18.8 1.7 35 46-80 5-43 (43)
295 PRK03681 hypA hydrogenase nick 33.4 37 0.0008 23.7 2.1 26 134-164 70-95 (114)
296 PF10122 Mu-like_Com: Mu-like 33.3 16 0.00035 21.4 0.3 29 135-165 5-33 (51)
297 PF07295 DUF1451: Protein of u 32.7 25 0.00054 25.8 1.2 11 206-216 129-139 (146)
298 smart00154 ZnF_AN1 AN1-like Zi 32.4 29 0.00064 19.0 1.2 17 157-173 13-29 (39)
299 PF14787 zf-CCHC_5: GAG-polypr 32.4 31 0.00067 18.7 1.2 18 165-182 3-20 (36)
300 TIGR00280 L37a ribosomal prote 32.3 51 0.0011 22.0 2.5 31 204-234 32-63 (91)
301 PF09151 DUF1936: Domain of un 31.3 23 0.0005 18.3 0.6 10 208-217 2-11 (36)
302 PF09723 Zn-ribbon_8: Zinc rib 31.3 35 0.00076 19.0 1.4 28 135-164 6-34 (42)
303 PF01363 FYVE: FYVE zinc finge 31.1 23 0.00049 21.9 0.7 33 134-172 9-41 (69)
304 COG2816 NPY1 NTP pyrophosphohy 30.8 55 0.0012 26.8 2.9 31 204-234 108-139 (279)
305 PTZ00255 60S ribosomal protein 30.5 65 0.0014 21.5 2.7 31 204-234 33-64 (90)
306 KOG2789 Putative Zn-finger pro 30.4 17 0.00038 31.0 0.1 36 45-81 72-107 (482)
307 PRK08332 ribonucleotide-diphos 30.4 33 0.00071 35.5 1.9 24 208-233 1705-1735(1740)
308 PF02068 Metallothio_PEC: Plan 30.3 26 0.00057 22.3 0.8 26 208-233 10-40 (76)
309 COG3529 Predicted nucleic-acid 30.3 15 0.00032 22.4 -0.3 25 209-233 12-41 (66)
310 PF10272 Tmpp129: Putative tra 29.9 75 0.0016 27.1 3.7 35 70-106 313-353 (358)
311 PF00569 ZZ: Zinc finger, ZZ t 28.9 53 0.0011 18.6 1.9 34 46-79 3-37 (46)
312 PF11781 RRN7: RNA polymerase 28.4 46 0.001 17.9 1.5 24 208-233 9-34 (36)
313 COG3677 Transposase and inacti 28.2 1.1E+02 0.0023 21.9 3.8 38 131-170 27-67 (129)
314 KOG2932 E3 ubiquitin ligase in 28.1 15 0.00033 30.3 -0.6 29 135-172 91-119 (389)
315 PF04423 Rad50_zn_hook: Rad50 28.1 87 0.0019 18.3 2.9 17 93-111 22-38 (54)
316 PRK03976 rpl37ae 50S ribosomal 27.9 67 0.0014 21.4 2.5 31 204-234 33-64 (90)
317 COG3809 Uncharacterized protei 27.9 38 0.00083 21.8 1.3 11 136-148 3-13 (88)
318 COG1996 RPC10 DNA-directed RNA 27.6 42 0.00092 19.6 1.3 15 204-218 21-35 (49)
319 cd04476 RPA1_DBD_C RPA1_DBD_C: 27.4 48 0.001 24.6 2.0 25 207-232 34-59 (166)
320 PF02148 zf-UBP: Zn-finger in 27.2 50 0.0011 20.1 1.7 32 50-83 1-36 (63)
321 cd00729 rubredoxin_SM Rubredox 26.5 66 0.0014 17.0 1.9 23 136-164 4-26 (34)
322 cd02249 ZZ Zinc finger, ZZ typ 26.5 81 0.0018 17.8 2.4 31 49-80 2-33 (46)
323 PF06221 zf-C2HC5: Putative zi 26.4 44 0.00094 20.2 1.3 12 157-168 19-30 (57)
324 KOG3005 GIY-YIG type nuclease 26.4 1.3E+02 0.0029 24.4 4.3 61 47-110 182-249 (276)
325 PF00412 LIM: LIM domain; Int 26.3 43 0.00094 19.5 1.3 33 46-80 25-57 (58)
326 PRK11032 hypothetical protein; 26.2 36 0.00077 25.4 1.1 13 205-217 140-152 (160)
327 PRK06386 replication factor A; 25.9 33 0.00072 29.2 1.0 14 206-219 235-248 (358)
328 PF13834 DUF4193: Domain of un 25.9 19 0.00041 24.4 -0.4 33 43-76 66-98 (99)
329 PRK07562 ribonucleotide-diphos 25.8 68 0.0015 32.0 3.1 28 203-232 1186-1215(1220)
330 COG2995 PqiA Uncharacterized p 25.3 60 0.0013 28.0 2.4 33 132-166 16-48 (418)
331 PF07649 C1_3: C1-like domain; 25.1 64 0.0014 16.2 1.7 28 49-76 2-29 (30)
332 TIGR02605 CxxC_CxxC_SSSS putat 25.0 63 0.0014 18.6 1.8 28 135-164 6-34 (52)
333 PF06044 DRP: Dam-replacing fa 24.9 18 0.00039 28.8 -0.7 31 134-166 31-63 (254)
334 PHA02325 hypothetical protein 24.8 42 0.0009 20.7 1.0 11 206-216 2-12 (72)
335 PF05515 Viral_NABP: Viral nuc 24.3 58 0.0013 23.1 1.8 23 204-226 59-81 (124)
336 COG1571 Predicted DNA-binding 23.7 46 0.00099 29.0 1.4 26 208-234 351-377 (421)
337 KOG1571 Predicted E3 ubiquitin 23.7 59 0.0013 27.5 2.0 25 46-73 304-328 (355)
338 PRK05580 primosome assembly pr 23.7 61 0.0013 30.3 2.3 26 208-233 391-417 (679)
339 PRK13130 H/ACA RNA-protein com 23.1 57 0.0012 19.7 1.3 36 91-128 17-52 (56)
340 KOG2462 C2H2-type Zn-finger pr 23.1 97 0.0021 25.3 3.0 60 45-106 159-228 (279)
341 PF04216 FdhE: Protein involve 22.8 31 0.00067 28.4 0.2 26 208-233 173-206 (290)
342 PRK00564 hypA hydrogenase nick 22.7 64 0.0014 22.6 1.8 26 134-164 71-96 (117)
343 KOG3183 Predicted Zn-finger pr 22.2 18 0.00038 28.7 -1.2 40 135-181 99-138 (250)
344 KOG2041 WD40 repeat protein [G 22.0 1.2E+02 0.0026 28.5 3.7 20 111-130 1088-1107(1189)
345 PLN02436 cellulose synthase A 21.8 75 0.0016 31.2 2.5 50 47-104 36-89 (1094)
346 PF04236 Transp_Tc5_C: Tc5 tra 21.7 66 0.0014 19.9 1.5 30 134-172 27-56 (63)
347 PF08882 Acetone_carb_G: Aceto 21.4 51 0.0011 22.9 1.0 12 208-219 75-86 (112)
348 PRK02935 hypothetical protein; 21.1 47 0.001 22.8 0.8 19 207-225 70-91 (110)
349 PF13465 zf-H2C2_2: Zinc-finge 21.0 65 0.0014 15.6 1.1 22 78-103 3-24 (26)
350 PF01194 RNA_pol_N: RNA polyme 21.0 1.2E+02 0.0027 18.5 2.5 14 90-105 3-16 (60)
351 PF10530 Toxin_35: Toxin with 20.8 50 0.0011 15.9 0.6 12 219-230 12-23 (23)
352 COG1675 TFA1 Transcription ini 20.7 84 0.0018 23.9 2.2 32 131-165 110-141 (176)
353 PF01783 Ribosomal_L32p: Ribos 20.6 1.2E+02 0.0026 18.1 2.5 25 131-164 23-47 (56)
354 COG1656 Uncharacterized conser 20.5 83 0.0018 23.6 2.1 16 132-149 95-110 (165)
355 PF03563 Bunya_G2: Bunyavirus 20.5 86 0.0019 25.4 2.3 30 204-234 231-260 (285)
356 PF14392 zf-CCHC_4: Zinc knuck 20.1 36 0.00077 19.6 0.1 17 165-181 32-48 (49)
357 PF12677 DUF3797: Domain of un 20.0 72 0.0016 18.5 1.3 29 206-234 12-48 (49)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.1e-36 Score=250.29 Aligned_cols=185 Identities=36% Similarity=0.838 Sum_probs=157.0
Q ss_pred CcccccccccCC-CCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHH
Q 048114 46 TSFICDICVEPK-STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNAL 124 (234)
Q Consensus 46 ~~~~C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~ 124 (234)
+..+|.||+.+. ....++....|+|.||.+|+++|++++.. ....++||...|...++.+....+|++++.++|++.+
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~-~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~ 223 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLL-SGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRL 223 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhc-cCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHH
Confidence 467899999444 44466777799999999999999999943 4568999999999999999999999999999999999
Q ss_pred HHHHHhCCCeecCCCCCCCCceecCCC---CccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHH
Q 048114 125 CEAVILGAQKFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTL 201 (234)
Q Consensus 125 ~~~~~~~~~~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~ 201 (234)
.+.++...+.+|||.++|...+...+. .......|+.|+..||..|+.+||.+.+|++|+++..+... .+..+..+
T Consensus 224 ~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~-d~~~~~~l 302 (384)
T KOG1812|consen 224 KEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYV-DDITLKYL 302 (384)
T ss_pred HHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccc-cHHHHHHH
Confidence 998888777779999999988876542 33445679999999999999999999999999999864432 23333333
Q ss_pred HhcCCcccCCCCCceeeeccCCCceEecCCCCC
Q 048114 202 AQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL 234 (234)
Q Consensus 202 ~~~~~~k~CP~C~~~i~k~~GCnhm~C~C~~~F 234 (234)
+ .+|+.||+|+.+|++++|||||+|+||++|
T Consensus 303 a--~~wr~CpkC~~~ie~~~GCnhm~CrC~~~f 333 (384)
T KOG1812|consen 303 A--KRWRQCPKCKFMIELSEGCNHMTCRCGHQF 333 (384)
T ss_pred H--HhcCcCcccceeeeecCCcceEEeeccccc
Confidence 3 899999999999999999999999999998
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-34 Score=233.70 Aligned_cols=190 Identities=26% Similarity=0.669 Sum_probs=155.4
Q ss_pred hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcC-CccccCCCCCCCCCCCHHHHhccCCHHHHHHHH
Q 048114 43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN-ITSINCPVADCKGVLEPEYCRDILPEDVFNRWG 121 (234)
Q Consensus 43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 121 (234)
.+...+.|.|||++..+...+.+++|+|.||+.|++.|+...|.+| +..++||.+.|+..-.+..++.++..+++++|+
T Consensus 180 F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 3567899999999998888888899999999999999999999998 678999999999999999999999999999999
Q ss_pred HHHHHHHHh-CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhH--------HHhhhccCC
Q 048114 122 NALCEAVIL-GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEF--------QKLHKDERE 192 (234)
Q Consensus 122 ~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~--------~~~~~~~~~ 192 (234)
+++.+..+. ..+.+|||++.|+.....+++ ...+.|.+|+..||..|+..||+...|.-- ..+.....+
T Consensus 260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~--~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRACCQLPVKQDPG--RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCccccCch--hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 998876664 678899999999998854433 456899999999999999999999999532 112111100
Q ss_pred -h-----------HH----HHHHHHHhcCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 193 -P-----------ED----IMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 193 -~-----------~~----~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
+ .+ ..+++-+...+.|+||+|+++|+|++|||||+|. ||+-|
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~f 396 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYF 396 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccc
Confidence 0 01 1122233456789999999999999999999995 88755
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=8.5e-29 Score=213.02 Aligned_cols=225 Identities=21% Similarity=0.443 Sum_probs=177.6
Q ss_pred ccccccCCCCCCcccCCCCCcccccccccCCCCcccchh--h--hcCCcccccccccCCCCCCceeeCCCCChhhHHHHH
Q 048114 3 ILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIE--E--RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMT 78 (234)
Q Consensus 3 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~ 78 (234)
+|.+++..+.+++..+.|+...+.+.....+...-.... . ......+|.||++.+.. ......|+|.||..||.
T Consensus 22 ~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~~~~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~ 99 (444)
T KOG1815|consen 22 ILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWPKKKGDVQCGICVESYDG--EIIGLGCGHPFCPPCWT 99 (444)
T ss_pred hhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccCCCCccccCCcccCCCcc--hhhhcCCCcHHHHHHHH
Confidence 577788888899999999998887666544443211111 0 12345899999998865 34456999999999999
Q ss_pred HHHHHHHhcCCc-cccCCCCCCCCCCCHHHHhccCCH-HHHHHHHHHHHHHHHhCCC-eecCCCCCCCCceecCCCCccC
Q 048114 79 KYVASKLQENIT-SINCPVADCKGVLEPEYCRDILPE-DVFNRWGNALCEAVILGAQ-KFYCPFKDCSALLIDDGGEAIR 155 (234)
Q Consensus 79 ~~~~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~~~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~ 155 (234)
.|+...|.++.. .|+||...|...+..+.|..++++ +..++|.+.+..+++.... ..|||.|+|+..+... .....
T Consensus 100 ~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~-~~~~~ 178 (444)
T KOG1815|consen 100 GYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFG-SLESV 178 (444)
T ss_pred HHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeecc-CCCcc
Confidence 999999988633 399999999999999999999888 5999999999998887544 5799999999987753 23345
Q ss_pred cccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeeeccCCCceEec---CCC
Q 048114 156 ESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS---SNP 232 (234)
Q Consensus 156 ~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~ 232 (234)
.+.|. |++.||+.|+.+||.+.+|..+..|........+ .+. ....++++||+|.++|+|++|||||+|. |++
T Consensus 179 ~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se-~~~--wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~ 254 (444)
T KOG1815|consen 179 EVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSE-TIN--WILANTKECPKCKVPIEKDGGCNHMTCKSASCKH 254 (444)
T ss_pred ceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhh-hhh--hhhccCccCCCcccchhccCCccccccccCCcCC
Confidence 58895 6779999999999999999999988764332211 111 3467889999999999999999999995 999
Q ss_pred CC
Q 048114 233 QL 234 (234)
Q Consensus 233 ~F 234 (234)
+|
T Consensus 255 ~F 256 (444)
T KOG1815|consen 255 EF 256 (444)
T ss_pred ee
Confidence 88
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=1.5e-25 Score=176.19 Aligned_cols=182 Identities=25% Similarity=0.573 Sum_probs=139.6
Q ss_pred cCCcccccccccCCCCCCceeeCCCC--ChhhHHHHHHHHHHHHhcCC--------ccccCCCCCCCCCCCHHH-HhccC
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCS--HSYCTECMTKYVASKLQENI--------TSINCPVADCKGVLEPEY-CRDIL 112 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~--------~~i~CP~~~C~~~l~~~~-i~~~l 112 (234)
+....+|..|-+.- +.+..++|. |..|.+|++.|..+.+++.. ..+.||. +|...+-.+. -..+|
T Consensus 218 N~~ni~C~~Ctdv~---~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 218 NSRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred ccccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 46688999997743 556667997 99999999999999987632 4678886 7876654332 23488
Q ss_pred CHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCcc-ccccccccCCCCCCCCCChhhHHH------
Q 048114 113 PEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPD-CNRMFCAQCKVPWHAGIRCAEFQK------ 185 (234)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~------ 185 (234)
..+.+.+|++...+..+...+.+.||+|+|++.+...+ +..++.|+. |++.||..|+..+|.| .|.+.-.
T Consensus 294 g~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~t 370 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTTT 370 (446)
T ss_pred chhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhccc-cceeeeccccccc
Confidence 99999999999999988888899999999999888765 356699987 9999999999999998 3432111
Q ss_pred ------hhhccCChHHHHHHHHHhcCCcccCCCCCceeeeccCCCceEec---CCCC
Q 048114 186 ------LHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS---SNPQ 233 (234)
Q Consensus 186 ------~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~ 233 (234)
....++..+++.. +...+..+|+||+|+++.||+|||.||.|. ||.+
T Consensus 371 c~y~vde~~a~~arwd~as-~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~e 426 (446)
T KOG0006|consen 371 CAYRVDERAAEQARWDAAS-KETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLE 426 (446)
T ss_pred eeeecChhhhhhhhhhhhh-hhhhhhccCCCCCccCccccCCceEEeecCCCCCCce
Confidence 1112222333332 334467889999999999999999999994 8865
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.34 E-value=1.8e-12 Score=81.99 Aligned_cols=63 Identities=35% Similarity=0.835 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHhC-CCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCCh
Q 048114 118 NRWGNALCEAVILG-AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC 180 (234)
Q Consensus 118 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 180 (234)
++|++++.+.++.. ++.+|||+++|+.++..........+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 36888888888775 5778999999999888764334567999999999999999999999987
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=99.26 E-value=1.1e-12 Score=82.94 Aligned_cols=63 Identities=29% Similarity=0.774 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHhC-CCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCCh
Q 048114 118 NRWGNALCEAVILG-AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC 180 (234)
Q Consensus 118 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 180 (234)
++|++++.+.++.. .+.+|||+++|+.++..+.......+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 35666666655543 4557999999999999876655445999999999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.88 E-value=4.6e-10 Score=64.15 Aligned_cols=40 Identities=28% Similarity=0.845 Sum_probs=28.0
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|+||++.+. +++++ +|||+||..|+.+++... +...+.||
T Consensus 1 CpiC~~~~~--~Pv~l-~CGH~FC~~Cl~~~~~~~---~~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFK--DPVSL-PCGHSFCRSCLERLWKEP---SGSGFSCP 40 (42)
T ss_dssp ETTTTSB-S--SEEE--SSSSEEEHHHHHHHHCCS---SSST---S
T ss_pred CCccchhhC--Ccccc-CCcCHHHHHHHHHHHHcc---CCcCCCCc
Confidence 899999986 66665 999999999999999643 12237888
No 8
>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=98.77 E-value=7e-09 Score=59.19 Aligned_cols=39 Identities=36% Similarity=1.044 Sum_probs=32.4
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|+||++.+. +...+++|||.||.+|+.++++. ...++||
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN-----SGSVKCP 39 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH-----TSSSBTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh-----cCCccCC
Confidence 799999876 44557799999999999999986 3466788
No 9
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.74 E-value=5.1e-09 Score=59.04 Aligned_cols=37 Identities=35% Similarity=1.055 Sum_probs=29.2
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|+||++.+. +++.+++|||.||.+|+.+|++. ..+||
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~-------~~~CP 37 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEK-------NPKCP 37 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHC-------TSB-T
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHC-------cCCCc
Confidence 899999876 56567899999999999999863 25788
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=98.74 E-value=2.9e-09 Score=61.79 Aligned_cols=40 Identities=25% Similarity=0.682 Sum_probs=32.2
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
+|+||++++..++.+..++|+|.||.+|+.+|++.. .+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP 41 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCP 41 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-T
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCC
Confidence 599999999655666666899999999999999653 2888
No 11
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.74 E-value=1.4e-08 Score=74.67 Aligned_cols=58 Identities=24% Similarity=0.704 Sum_probs=45.7
Q ss_pred hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
..+..+.|+||++.+....++.. .|||.||+.|++..+. ...+|| .|...++..++..
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk-------~~~~CP--~C~kkIt~k~~~r 184 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALK-------NTNKCP--TCRKKITHKQFHR 184 (187)
T ss_pred ccccccCCCceecchhhcccccc-ccchhHHHHHHHHHHH-------hCCCCC--Ccccccchhhhee
Confidence 34667899999999986565554 9999999999998885 345899 7877888776654
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.70 E-value=2.2e-08 Score=57.98 Aligned_cols=43 Identities=33% Similarity=0.877 Sum_probs=35.8
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK 100 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 100 (234)
.|+||++.+.....+.+++|||+||..|+.+.. ...+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCc--CCC
Confidence 499999999656678888999999999998887 3567899 665
No 13
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.68 E-value=1.3e-08 Score=58.10 Aligned_cols=43 Identities=26% Similarity=0.709 Sum_probs=24.1
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|+||.+.....+.+.+++|||.||.+|++++..... ...++||
T Consensus 1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCccccccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999334455666679999999999999997432 3567887
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.63 E-value=3.6e-08 Score=74.38 Aligned_cols=64 Identities=22% Similarity=0.527 Sum_probs=47.9
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHH---------hcCCccccCCCCCCCCCCCHHHHhccCC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKL---------QENITSINCPVADCKGVLEPEYCRDILP 113 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i---------~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 113 (234)
...++|+||++.+. +++. +.|||.||..|+.+|+...- ........|| .|+..++...+..+..
T Consensus 16 ~~~~~CpICld~~~--dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiyg 88 (193)
T PLN03208 16 GGDFDCNICLDQVR--DPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYG 88 (193)
T ss_pred CCccCCccCCCcCC--CcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeec
Confidence 45788999999874 5444 59999999999999976421 1123467999 9999999877766543
No 15
>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=98.49 E-value=1.8e-07 Score=54.08 Aligned_cols=44 Identities=32% Similarity=0.823 Sum_probs=34.6
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV 102 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 102 (234)
+|+||++.+. +.+.+.+|+|.||..|+..|+.. ....|| .|+..
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence 4999999873 55666679999999999999874 346799 77654
No 16
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.40 E-value=2.3e-07 Score=55.24 Aligned_cols=46 Identities=28% Similarity=0.764 Sum_probs=35.3
Q ss_pred cccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...|.||++... + +.+.+|||. ||.+|+.+++. ...+|| .|+..+.
T Consensus 2 ~~~C~iC~~~~~--~-~~~~pCgH~~~C~~C~~~~~~-------~~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--D-VVLLPCGHLCFCEECAERLLK-------RKKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--S-EEEETTCEEEEEHHHHHHHHH-------TTSBBT--TTTBB-S
T ss_pred cCCCccCCccCC--c-eEEeCCCChHHHHHHhHHhcc-------cCCCCC--cCChhhc
Confidence 457999999763 3 555699999 99999999997 356899 8887654
No 17
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=2.7e-06 Score=70.43 Aligned_cols=111 Identities=18% Similarity=0.472 Sum_probs=67.9
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNA 123 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~ 123 (234)
....++|+||++.+... .+++|+|.||..|+...+. ..+.|| .|.. ... .+............
T Consensus 10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr~-~~~----~~~~n~~l~~~~~~ 72 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCRP-PSR----NLRPNVLLANLVER 72 (386)
T ss_pred ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccCC-chh----ccCccHHHHHHHHH
Confidence 45688999999999733 5669999999999999997 458999 7773 221 22222222222222
Q ss_pred HHHHHHhCC-Ce--ecCCCCCCCCceecCCCCccCcccCccccccccccCC-CCCCCCCChhh
Q 048114 124 LCEAVILGA-QK--FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCK-VPWHAGIRCAE 182 (234)
Q Consensus 124 ~~~~~~~~~-~~--~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C~~ 182 (234)
......... .. ..|+ .......+.|..|+..+|..|. ...|.++.-..
T Consensus 73 ~~~~~~~~~~~~~~~~c~-----------~~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~ 124 (386)
T KOG2177|consen 73 LRQLRLSRPLGSKEELCE-----------KHGEELKLFCEEDEKLLCVLCRESGEHRGHPVLP 124 (386)
T ss_pred HHhcCCcccccccchhhh-----------hcCCcceEEecccccccCCCCCCcccccCCcccc
Confidence 221111100 00 0233 1111144889999999999998 56787766543
No 18
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.17 E-value=1e-06 Score=69.93 Aligned_cols=52 Identities=29% Similarity=0.775 Sum_probs=41.1
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC 108 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 108 (234)
+....|.+|++... .++.++|||.||..|+..|...+- .|| -|...+.+..+
T Consensus 237 ~a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~-------eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKA-------ECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHcccc-------CCC--cccccCCCcce
Confidence 45688999999763 455679999999999999997442 299 89888877654
No 19
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.17 E-value=2.7e-06 Score=47.25 Aligned_cols=37 Identities=30% Similarity=0.889 Sum_probs=28.3
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|+||++.. ....+++|+|.||..|+..|+. .....||
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~------~~~~~CP 37 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLK------SGNNTCP 37 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHH------hCcCCCC
Confidence 78999873 3444569999999999999987 1245677
No 20
>PHA02926 zinc finger-like protein; Provisional
Probab=98.17 E-value=2.8e-06 Score=65.11 Aligned_cols=58 Identities=24% Similarity=0.580 Sum_probs=41.3
Q ss_pred cCCcccccccccCCCC-----C-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 44 IETSFICDICVEPKST-----D-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~-----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
.++..+|+||+|..-. . ..-.+.+|+|.||..|++.|....-..+ ..-.|| .|+..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP--iCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP--ICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC--CCcceee
Confidence 4567899999997621 1 1234679999999999999998653222 345799 7876543
No 21
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.11 E-value=4.4e-06 Score=52.22 Aligned_cols=51 Identities=20% Similarity=0.249 Sum_probs=40.0
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
+.|+||++.+. +++. .+|||.||+.|+.+|+.. ...|| .|+..++.+++..
T Consensus 2 ~~Cpi~~~~~~--~Pv~-~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMK--DPVI-LPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCC--CCEE-CCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhcee
Confidence 56999999875 5554 599999999999999964 24789 7888887665443
No 22
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=3e-06 Score=65.30 Aligned_cols=59 Identities=22% Similarity=0.639 Sum_probs=45.9
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL 112 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l 112 (234)
...++|.||+|.-. +++ +..|||.||..||-+|+..+.. .-.|| .|+..++.+.+-.+.
T Consensus 45 ~~~FdCNICLd~ak--dPV-vTlCGHLFCWpClyqWl~~~~~----~~~cP--VCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 45 GGFFDCNICLDLAK--DPV-VTLCGHLFCWPCLYQWLQTRPN----SKECP--VCKAEVSIDTVVPLY 103 (230)
T ss_pred CCceeeeeeccccC--CCE-EeecccceehHHHHHHHhhcCC----CeeCC--ccccccccceEEeee
Confidence 56899999999653 544 4589999999999999986633 33578 899888887766554
No 23
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=2.3e-06 Score=72.96 Aligned_cols=59 Identities=24% Similarity=0.589 Sum_probs=46.9
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL 112 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l 112 (234)
...||||+++.+ ...++.|||.||..||.+|+.... ....-.|| -|...+.+.++..+.
T Consensus 186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~--~~~~~~CP--iC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSA--IKGPCSCP--ICRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhc--ccCCccCC--chhhhccccceeeee
Confidence 789999999875 233457999999999999998772 23467899 899999887777654
No 24
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.07 E-value=4.3e-06 Score=65.92 Aligned_cols=51 Identities=25% Similarity=0.626 Sum_probs=37.8
Q ss_pred CCcccccccccCCCCCC-----ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDE-----SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
.+..+|+||++.+.... ...+++|+|.||.+|+..|... .-.|| .|+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCC--CCCCEee
Confidence 44678999999875322 1345689999999999999852 23799 7876554
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.07 E-value=3.9e-06 Score=70.89 Aligned_cols=68 Identities=24% Similarity=0.633 Sum_probs=49.0
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh-ccCCHHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR-DILPEDVFNRWGN 122 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~~ 122 (234)
++..+.|+||++.+. +++ +++|+|.||..|+..|+.. ...|| .|...+....+. +.+-.++++.|..
T Consensus 23 Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~-------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 23 LDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSN-------QPKCP--LCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred cccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhC-------CCCCC--CCCCccccccCccchHHHHHHHHHHH
Confidence 566889999999885 444 4699999999999999853 23799 898887654433 3444556666654
Q ss_pred H
Q 048114 123 A 123 (234)
Q Consensus 123 ~ 123 (234)
.
T Consensus 91 ~ 91 (397)
T TIGR00599 91 L 91 (397)
T ss_pred h
Confidence 3
No 26
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.01 E-value=3.1e-06 Score=68.49 Aligned_cols=66 Identities=23% Similarity=0.592 Sum_probs=51.1
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWG 121 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~ 121 (234)
++..+.|.||++.|. .+.+.+|+|.||.-|++.|+. ..-.|| .|...+....++. .+-.++++.|.
T Consensus 20 lD~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~-------~~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLS-------YKPQCP--TCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred hHHHHHHhHHHHHhc---CceeccccchHHHHHHHHHhc-------cCCCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence 455778999999984 455669999999999999996 345799 8988888888775 45566666664
No 27
>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=97.85 E-value=5.2e-05 Score=61.68 Aligned_cols=56 Identities=25% Similarity=0.564 Sum_probs=39.8
Q ss_pred cccccccccCCCCCCc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 47 SFICDICVEPKSTDES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
...||+|..+...+.. +.+.+|||.||..|+...+. .+ +..|| .|+..+....++.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~--~~~CP--~C~~~lrk~~fr~ 60 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG--SGSCP--ECDTPLRKNNFRV 60 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC--CCCCC--CCCCccchhhccc
Confidence 3569999986432222 22227999999999999873 22 35899 9998888876554
No 28
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.69 E-value=3.7e-05 Score=61.50 Aligned_cols=54 Identities=22% Similarity=0.667 Sum_probs=45.0
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP 105 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 105 (234)
.....+|.||++.+...+.+..++|.|.|...|+.+|+. | ...+|| .|...+++
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~-----~-y~~~CP--vCrt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL-----G-YSNKCP--VCRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHh-----h-hcccCC--ccCCCCCC
Confidence 456789999999998777777889999999999999995 2 356899 89887764
No 29
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.50 E-value=7.2e-06 Score=50.24 Aligned_cols=51 Identities=25% Similarity=0.712 Sum_probs=24.8
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 107 (234)
++....|++|.+.+. .++.+..|.|.||..|+...+. -.|| .|..+--..+
T Consensus 4 le~lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD 54 (65)
T PF14835_consen 4 LEELLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQD 54 (65)
T ss_dssp HHHTTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS
T ss_pred HHHhcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHH
Confidence 445678999999875 7777789999999999966431 2499 7876544333
No 30
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.49 E-value=8.1e-05 Score=61.59 Aligned_cols=46 Identities=28% Similarity=0.726 Sum_probs=39.3
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
.+|.||+|++..++.+..++|+|.|...|+..|+... .=.|| .|+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CP--vCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCP--VCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCC--CCCC
Confidence 6899999999988888889999999999999999744 23599 6665
No 31
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.40 E-value=0.00012 Score=44.59 Aligned_cols=47 Identities=32% Similarity=0.731 Sum_probs=33.1
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK 100 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 100 (234)
.+.|||-+..+. +++....|+|.|-++-+.+|+ .+...+.||..+|.
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 678999999886 888878999999999999999 33467899988884
No 32
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.00024 Score=56.00 Aligned_cols=54 Identities=24% Similarity=0.555 Sum_probs=40.2
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC 108 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 108 (234)
...+.|.||++... .+..++|||.||..|+...++.+ ..-.|| .|.....+..+
T Consensus 213 ~~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKK-----KYEFCP--LCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccC---CcccccccchhhHHHHHHHHHhh-----ccccCc--hhhhhccchhh
Confidence 34788999999763 45556999999999999854322 244699 88888777665
No 33
>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=97.32 E-value=0.00012 Score=47.06 Aligned_cols=40 Identities=25% Similarity=0.710 Sum_probs=28.9
Q ss_pred cccccccCCCC----------CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 49 ICDICVEPKST----------DESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 49 ~C~iC~~~~~~----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
.|.||++++.. .-.+....|||.|...||.+|++.+ -.||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP 70 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCP 70 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-T
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCC
Confidence 49999999921 1234456899999999999999532 2888
No 34
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00014 Score=65.16 Aligned_cols=57 Identities=21% Similarity=0.620 Sum_probs=45.1
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhcc
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDI 111 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 111 (234)
.....+|++|.+.. +...+..|+|.||..|++..+... .=+|| .|...|+..+|..+
T Consensus 640 yK~~LkCs~Cn~R~---Kd~vI~kC~H~FC~~Cvq~r~etR------qRKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 640 YKELLKCSVCNTRW---KDAVITKCGHVFCEECVQTRYETR------QRKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred HHhceeCCCccCch---hhHHHHhcchHHHHHHHHHHHHHh------cCCCC--CCCCCCCccccccc
Confidence 46688999998543 344456999999999999988654 34899 99999999888754
No 35
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.22 E-value=0.00054 Score=42.69 Aligned_cols=30 Identities=23% Similarity=0.698 Sum_probs=26.6
Q ss_pred CCcccCC--CCCceeeecc--CCCceEe-cCCCCC
Q 048114 205 ENWRRCP--NCKIFVEKKE--GCRYMRC-SSNPQL 234 (234)
Q Consensus 205 ~~~k~CP--~C~~~i~k~~--GCnhm~C-~C~~~F 234 (234)
.+++.|| +|+..|+..+ |.++|+| .||+.|
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 5789999 9999999964 9999999 699887
No 36
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.06 E-value=0.00031 Score=60.43 Aligned_cols=56 Identities=27% Similarity=0.730 Sum_probs=42.3
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
.....+|.+|-++-. +.+. ..|.|.||+-|++.|+..... +. .+.|| .|...|+.+
T Consensus 533 nk~~~~C~lc~d~ae--d~i~-s~ChH~FCrlCi~eyv~~f~~-~~-nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 533 NKGEVECGLCHDPAE--DYIE-SSCHHKFCRLCIKEYVESFME-NN-NVTCP--VCHIGLSID 588 (791)
T ss_pred ccCceeecccCChhh--hhHh-hhhhHHHHHHHHHHHHHhhhc-cc-CCCCc--ccccccccc
Confidence 355778999988643 4444 599999999999999976643 32 49999 887776665
No 37
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.02 E-value=0.00043 Score=55.20 Aligned_cols=67 Identities=18% Similarity=0.418 Sum_probs=45.7
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWGN 122 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~~ 122 (234)
++....|.||-+.+. .+...+|||.||.-|++.|+.. .-.|| .|....-...++. .+..+..+.|..
T Consensus 22 LDs~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~-------qp~CP--~Cr~~~~esrlr~~s~~~ei~es~~~ 89 (391)
T COG5432 22 LDSMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGT-------QPFCP--VCREDPCESRLRGSSGSREINESHAR 89 (391)
T ss_pred chhHHHhhhhhheee---cceecccccchhHHHHHHHhcC-------CCCCc--cccccHHhhhcccchhHHHHHHhhhh
Confidence 455677999988774 4556799999999999999952 23588 7766544444443 344555555543
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.00 E-value=0.00032 Score=44.68 Aligned_cols=57 Identities=18% Similarity=0.457 Sum_probs=26.5
Q ss_pred cccccccccCCC-CCCcee-e---CCCCChhhHHHHHHHHHHHHhcC--Ccc--ccCCCCCCCCCCCH
Q 048114 47 SFICDICVEPKS-TDESFS-I---KGCSHSYCTECMTKYVASKLQEN--ITS--INCPVADCKGVLEP 105 (234)
Q Consensus 47 ~~~C~iC~~~~~-~~~~~~-~---~~C~H~fC~~Cl~~~~~~~i~~~--~~~--i~CP~~~C~~~l~~ 105 (234)
..+|+||++.+. .+.... . ..|+..|...||.+|+...-... ..+ =.|| .|...|+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 457999999865 222221 1 37899999999999998764432 222 2699 89887654
No 39
>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=97.00 E-value=0.00039 Score=44.75 Aligned_cols=51 Identities=16% Similarity=0.296 Sum_probs=36.3
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 107 (234)
..+.|+|+.+-+. +++.+ ++||+|.+.++.+|+.. ....|| .++..++..+
T Consensus 3 ~~f~CpIt~~lM~--dPVi~-~~G~tyer~~I~~~l~~------~~~~~P--~t~~~l~~~~ 53 (73)
T PF04564_consen 3 DEFLCPITGELMR--DPVIL-PSGHTYERSAIERWLEQ------NGGTDP--FTRQPLSESD 53 (73)
T ss_dssp GGGB-TTTSSB-S--SEEEE-TTSEEEEHHHHHHHHCT------TSSB-T--TT-SB-SGGG
T ss_pred cccCCcCcCcHhh--CceeC-CcCCEEcHHHHHHHHHc------CCCCCC--CCCCcCCccc
Confidence 4788999999875 66665 89999999999999964 345788 6777777653
No 40
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.0021 Score=51.06 Aligned_cols=51 Identities=29% Similarity=0.650 Sum_probs=38.8
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
....+|++|.+.-. .+....+|+|.||..|+..-.... ..+.|| .|+....
T Consensus 237 t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp--~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWD-----ASFTCP--LCGENVE 287 (298)
T ss_pred cCCceeeccCCCCC--CCeeeccccceeehhhhhhhhcch-----hhcccC--ccCCCCc
Confidence 34778999988643 566666899999999998776432 358999 8887655
No 41
>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=96.55 E-value=0.00073 Score=42.06 Aligned_cols=31 Identities=35% Similarity=0.948 Sum_probs=20.0
Q ss_pred cCCcccCCC--CCceeeeccCCCc--eEec-CCCCC
Q 048114 204 KENWRRCPN--CKIFVEKKEGCRY--MRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~--C~~~i~k~~GCnh--m~C~-C~~~F 234 (234)
...++.||+ |...|++.+|.++ |+|. |+++|
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 345689987 9999999999999 9997 99876
No 42
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.33 E-value=0.004 Score=51.58 Aligned_cols=53 Identities=19% Similarity=0.519 Sum_probs=38.4
Q ss_pred CCcccccccccCC-CCC---------CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 45 ETSFICDICVEPK-STD---------ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 45 ~~~~~C~iC~~~~-~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
.....|.||+|+. ..+ ..+..++|||.+...|++.|++.+ -.|| .|+.++-.+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCP--ICr~p~ifd 347 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCP--ICRRPVIFD 347 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCC--cccCccccc
Confidence 4467899999994 322 123456999999999999999733 4799 788764443
No 43
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.32 E-value=0.0033 Score=52.41 Aligned_cols=57 Identities=28% Similarity=0.588 Sum_probs=40.3
Q ss_pred CCcccccccccCCCCCC-----ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDE-----SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
....+|.||++...... .-.+++|.|.||..|++.|-...-.+....-.|| .|....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CRv~s 220 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCRVPS 220 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--cccCcc
Confidence 45789999999885333 2234689999999999999855433333456899 776543
No 44
>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=96.22 E-value=0.0023 Score=32.17 Aligned_cols=23 Identities=22% Similarity=0.548 Sum_probs=17.4
Q ss_pred ccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
|.||.|+..|..+ -+.|. |||.|
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 5799999988543 46775 99887
No 45
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.01 E-value=0.0035 Score=51.14 Aligned_cols=51 Identities=27% Similarity=0.764 Sum_probs=39.4
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP 105 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 105 (234)
+.+-.+|.+|-..+. +...+..|-|+||++||-.|++. ...|| .|...+..
T Consensus 12 ~n~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~~-------~~~CP--~C~i~ih~ 62 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLEE-------SKYCP--TCDIVIHK 62 (331)
T ss_pred cccceehhhccceee--cchhHHHHHHHHHHHHHHHHHHH-------hccCC--ccceeccC
Confidence 355789999998876 44455699999999999999975 45799 77655444
No 46
>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=95.75 E-value=0.024 Score=33.31 Aligned_cols=41 Identities=20% Similarity=0.636 Sum_probs=29.1
Q ss_pred cccccccCCCCCCceeeCCCC-----ChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 49 ICDICVEPKSTDESFSIKGCS-----HSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
.|-||++.....+.. ..+|. |.+..+||.+|+...- ..+||
T Consensus 1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~-----~~~C~ 46 (49)
T smart00744 1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESG-----NKTCE 46 (49)
T ss_pred CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcC-----CCcCC
Confidence 388999844444444 45885 7899999999997552 34787
No 47
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.69 E-value=0.0083 Score=50.76 Aligned_cols=35 Identities=26% Similarity=0.610 Sum_probs=27.9
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA 82 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 82 (234)
++.+.|+||..-+. +++. ++|+|..|+.|.+....
T Consensus 2 eeelkc~vc~~f~~--epii-l~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYR--EPII-LPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhcc--CceE-eecccHHHHHHHHhhcc
Confidence 45677999998875 5555 49999999999987654
No 48
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.46 E-value=0.036 Score=45.72 Aligned_cols=122 Identities=18% Similarity=0.375 Sum_probs=64.2
Q ss_pred cccccccccCCCCC---CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC--CCHHHHhccCCHHHHHHHH
Q 048114 47 SFICDICVEPKSTD---ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV--LEPEYCRDILPEDVFNRWG 121 (234)
Q Consensus 47 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--l~~~~i~~~l~~~~~~~~~ 121 (234)
...|.||-++++.. ..+..+.|||.+|..|+...+. ...+.|| .|... +....++.+-..-..-...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~------~~~i~cp--fcR~~~~~~~~~~~~l~kNf~ll~~~ 74 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG------NSRILCP--FCRETTEIPDGDVKSLQKNFALLQAI 74 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc------Cceeecc--CCCCcccCCchhHhhhhhhHHHHHHH
Confidence 45799999999643 3455679999999999988774 2356777 78777 4444554433222221111
Q ss_pred HHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCC-CCCC
Q 048114 122 NALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVP-WHAG 177 (234)
Q Consensus 122 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~H~~ 177 (234)
.......+.......+| +.|..............-.|......+|..|... .|.+
T Consensus 75 ~~~~~~~~~~~~~~~~~-~~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~~~~~ 130 (296)
T KOG4185|consen 75 EHMKKTTVEEKGEADSP-PKCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFGIHKG 130 (296)
T ss_pred HHHhcccccccCcccCC-cccccCcccccceeecCCCcchhhhhhhhhccchhhhhh
Confidence 11111111111122233 1255332221111111224566667788888764 3444
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=95.31 E-value=0.012 Score=34.99 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=21.0
Q ss_pred ccCCCCCceeeecc--CCCceEec-CCCCC
Q 048114 208 RRCPNCKIFVEKKE--GCRYMRCS-SNPQL 234 (234)
Q Consensus 208 k~CP~C~~~i~k~~--GCnhm~C~-C~~~F 234 (234)
+.||.|+.++...+ +-+++.|. |||+|
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46999999887654 35699996 99975
No 50
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.29 E-value=0.014 Score=50.25 Aligned_cols=53 Identities=21% Similarity=0.651 Sum_probs=38.8
Q ss_pred cCCcccccccccCCCCCC--------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 44 IETSFICDICVEPKSTDE--------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~--------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
++.+..|.||+.+++.-. ...+.+|.|.|.+.|+++|+. + ..+.|| .|...|+
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd-----~-ykl~CP--vCR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD-----T-YKLICP--VCRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh-----h-hcccCC--ccCCCCC
Confidence 466788999999885211 123569999999999999995 2 257899 6665554
No 51
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.24 E-value=0.016 Score=51.93 Aligned_cols=48 Identities=21% Similarity=0.600 Sum_probs=36.2
Q ss_pred CCcccccccccCCCCCCc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
.....|.||.|++..... ...++|+|.|+..|+++|++. .-.|| .|..
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-------~qtCP--~CR~ 338 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-------QQTCP--TCRT 338 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-------hCcCC--cchh
Confidence 447789999999863221 455699999999999999986 23688 5554
No 52
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.22 E-value=0.004 Score=53.12 Aligned_cols=105 Identities=19% Similarity=0.430 Sum_probs=62.7
Q ss_pred CcccccccccCCCCC---Cc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHH
Q 048114 46 TSFICDICVEPKSTD---ES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW 120 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~---~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 120 (234)
+...|+.++...... +. .....|+-.||.+|-..|-. .++-++++.+.++.....
T Consensus 237 p~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~-------------------~~sC~eykk~~~~~~~d~- 296 (384)
T KOG1812|consen 237 PYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA-------------------NLSCEEYKKLNPEEYVDD- 296 (384)
T ss_pred CCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC-------------------CCCHHHHHHhCCcccccH-
Confidence 455677776654321 11 11236666677777654431 144456666554332221
Q ss_pred HHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCC
Q 048114 121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIR 179 (234)
Q Consensus 121 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~ 179 (234)
.....+. ...+.|| .|...+....+ .+.+.|. |++.||+.|+..|+.+..
T Consensus 297 ---~~~~~la-~~wr~Cp--kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 297 ---ITLKYLA-KRWRQCP--KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred ---HHHHHHH-HhcCcCc--ccceeeeecCC--cceEEee-ccccchhhcCcchhhCCc
Confidence 1112222 4567899 99988876554 6779998 999999999999866543
No 53
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.19 E-value=0.023 Score=33.02 Aligned_cols=46 Identities=24% Similarity=0.636 Sum_probs=21.1
Q ss_pred ccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 50 CDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 50 C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
|++|.+++...+ .+.--+|+..+|+.|+.+... + ..=+|| .|+...
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~-----~-~~g~CP--gCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE-----N-EGGRCP--GCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT-----S-S-SB-T--TT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh-----c-cCCCCC--CCCCCC
Confidence 789999884333 333347899999999977664 1 133789 887653
No 54
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.17 E-value=0.027 Score=36.92 Aligned_cols=52 Identities=23% Similarity=0.611 Sum_probs=35.5
Q ss_pred cccccccccCCCCC---------C-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 47 SFICDICVEPKSTD---------E-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 47 ~~~C~iC~~~~~~~---------~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...|+||...|+.. + ++..-.|+|.|..-|+.+|+.++-. .=.|| -|.+.+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CP--mCR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCP--MCRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCC--CcCCeee
Confidence 44588887777521 1 3344589999999999999986521 23799 6776543
No 55
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.15 E-value=0.0028 Score=52.10 Aligned_cols=52 Identities=27% Similarity=0.746 Sum_probs=37.9
Q ss_pred hhcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 42 ERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 42 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
..+...+.|+||++-+. .......|.|.||.+|+..-+. .+ .=.|| .|...+
T Consensus 38 ~~~~~~v~c~icl~llk--~tmttkeClhrfc~~ci~~a~r----~g--n~ecp--tcRk~l 89 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLK--KTMTTKECLHRFCFDCIWKALR----SG--NNECP--TCRKKL 89 (381)
T ss_pred HHhhhhhccHHHHHHHH--hhcccHHHHHHHHHHHHHHHHH----hc--CCCCc--hHHhhc
Confidence 34677889999999875 4445569999999999977664 33 22588 776543
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.13 E-value=0.029 Score=45.61 Aligned_cols=94 Identities=22% Similarity=0.588 Sum_probs=55.9
Q ss_pred CCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCce
Q 048114 67 GCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL 146 (234)
Q Consensus 67 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~ 146 (234)
.||-.||++|++.|-...-..+... . -...|...+++... ...+|..+..+.+ .....-|| .|....
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~a-s-~t~tc~y~vde~~a-------~~arwd~as~~TI--k~tTkpCP--kChvpt 407 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEA-S-GTTTCAYRVDERAA-------EQARWDAASKETI--KKTTKPCP--KCHVPT 407 (446)
T ss_pred CchhHhHHHHHhhhccccceeeecc-c-cccceeeecChhhh-------hhhhhhhhhhhhh--hhccCCCC--CccCcc
Confidence 4889999999998875332221100 0 00135544444322 2345555544322 22345688 898777
Q ss_pred ecCCCCccCcccCcc--ccccccccCCCCCC
Q 048114 147 IDDGGEAIRESVCPD--CNRMFCAQCKVPWH 175 (234)
Q Consensus 147 ~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H 175 (234)
.+++. ...+.|+. |+..+|+.|+-+|.
T Consensus 408 ErnGG--CmHm~Ct~~~Cg~eWCw~C~tEW~ 436 (446)
T KOG0006|consen 408 ERNGG--CMHMKCTQPQCGLEWCWNCGTEWN 436 (446)
T ss_pred ccCCc--eEEeecCCCCCCceeEeccCChhh
Confidence 66543 34578865 99999999999884
No 57
>PHA00626 hypothetical protein
Probab=95.13 E-value=0.017 Score=34.23 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=21.6
Q ss_pred cCCCCCc-eeeeccCCCc----eEec-CCCCC
Q 048114 209 RCPNCKI-FVEKKEGCRY----MRCS-SNPQL 234 (234)
Q Consensus 209 ~CP~C~~-~i~k~~GCnh----m~C~-C~~~F 234 (234)
.||+|+. -|.|.+-|+. -.|. |||.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 5889887765 7895 99987
No 58
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.11 E-value=0.027 Score=46.67 Aligned_cols=49 Identities=31% Similarity=0.663 Sum_probs=36.2
Q ss_pred cCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
.+...+|.||+++.. ...+++|.|. .|.+|.+...- ..+ .|| .|...+.
T Consensus 287 ~~~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~---q~n----~CP--ICRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRY---QTN----NCP--ICRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHH---hhc----CCC--ccccchH
Confidence 366889999999863 4556699999 99999987652 122 589 8877654
No 59
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.049 Score=45.94 Aligned_cols=112 Identities=21% Similarity=0.497 Sum_probs=68.3
Q ss_pred CCcccccc--cccCC---CCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC-----C-
Q 048114 45 ETSFICDI--CVEPK---STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL-----P- 113 (234)
Q Consensus 45 ~~~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l-----~- 113 (234)
.....||- |..+. +...+.....|.-+||..|...|- |.. .|+...+ +.++-++ +
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H------G~s-------~Ck~~~~-~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH------GVS-------PCKVKAE-KLIELYLEYLEADE 336 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc------CCC-------cccCchH-HHHHHHHHHhhcCH
Confidence 44567887 55442 122344456889999999998876 221 3544322 2222111 1
Q ss_pred ---HHHHHHHHHHHHHHHHh--------CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC
Q 048114 114 ---EDVFNRWGNALCEAVIL--------GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW 174 (234)
Q Consensus 114 ---~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 174 (234)
.++..+|-+++.+..+. ..+...|| .|...+.+.++ .+++.|..|++.||+.|....
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG--CnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG--CNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC--ccceeeccccccceeehhhhc
Confidence 23445565444333222 23445899 99999887654 566999999999999998754
No 60
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=94.76 E-value=0.044 Score=53.23 Aligned_cols=69 Identities=20% Similarity=0.441 Sum_probs=53.6
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcC---CccccCCCCCCCCCCCHHHHhccCCH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN---ITSINCPVADCKGVLEPEYCRDILPE 114 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~~l~~ 114 (234)
.+..-.|.|||.+-....+...+.|+|.|...|.+..++..-..- ...|.|| .|..++..-.++++|++
T Consensus 3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence 355678999998765555555569999999999998887654331 2468999 99999999888888874
No 61
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=94.71 E-value=0.034 Score=47.69 Aligned_cols=52 Identities=21% Similarity=0.750 Sum_probs=38.3
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
++..+.|++|...+. +++....|||.||..|+..+... ...|| .|...+...
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~-------~~~cp--~~~~~~~~~ 69 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN-------HQKCP--VCRQELTQA 69 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc-------CcCCc--ccccccchh
Confidence 466889999999886 55543599999999999988864 45677 565444433
No 62
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.62 E-value=0.036 Score=47.31 Aligned_cols=49 Identities=29% Similarity=0.767 Sum_probs=36.7
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
+...++|.||+..+. .++.. +|||+||..|+.+-. . ....|| .|...+.
T Consensus 81 ~~sef~c~vc~~~l~--~pv~t-pcghs~c~~Cl~r~l----d---~~~~cp--~Cr~~l~ 129 (398)
T KOG4159|consen 81 IRSEFECCVCSRALY--PPVVT-PCGHSFCLECLDRSL----D---QETECP--LCRDELV 129 (398)
T ss_pred ccchhhhhhhHhhcC--CCccc-cccccccHHHHHHHh----c---cCCCCc--ccccccc
Confidence 366899999998875 55555 999999999977722 2 345788 6877666
No 63
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.022 Score=46.02 Aligned_cols=52 Identities=17% Similarity=0.353 Sum_probs=37.6
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 109 (234)
..+|.||+.+-. .+ +.+.|+|.||.-|++.-+.. ....|+ -|...++...+.
T Consensus 7 ~~eC~IC~nt~n--~P-v~l~C~HkFCyiCiKGsy~n------dk~~Ca--vCR~pids~i~~ 58 (324)
T KOG0824|consen 7 KKECLICYNTGN--CP-VNLYCFHKFCYICIKGSYKN------DKKTCA--VCRFPIDSTIDF 58 (324)
T ss_pred CCcceeeeccCC--cC-ccccccchhhhhhhcchhhc------CCCCCc--eecCCCCcchhc
Confidence 557999998753 33 45699999999999876541 234588 888887765443
No 64
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.35 E-value=0.022 Score=43.13 Aligned_cols=33 Identities=27% Similarity=0.826 Sum_probs=26.4
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYV 81 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 81 (234)
-.+.|.||-.++. .++ ...|||.||..|...-+
T Consensus 195 IPF~C~iCKkdy~--spv-vt~CGH~FC~~Cai~~y 227 (259)
T COG5152 195 IPFLCGICKKDYE--SPV-VTECGHSFCSLCAIRKY 227 (259)
T ss_pred Cceeehhchhhcc--chh-hhhcchhHHHHHHHHHh
Confidence 3678999999985 444 45999999999986655
No 65
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.25 E-value=0.049 Score=45.78 Aligned_cols=61 Identities=18% Similarity=0.384 Sum_probs=49.6
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
.-.-|.|||=-+.-+.++++..+.|||.++++=+.+..+ +|...++|| .|+..-..+..++
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq 391 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ 391 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence 455789999988888888888889999999998877765 555689999 9998777766554
No 66
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.11 E-value=0.018 Score=45.21 Aligned_cols=49 Identities=24% Similarity=0.611 Sum_probs=35.9
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 107 (234)
-..|..|+---+ .+.+.++.|.|.||..|...-. +-.|| .|+..+....
T Consensus 3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~---------~~~C~--lCkk~ir~i~ 51 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS---------PDVCP--LCKKSIRIIQ 51 (233)
T ss_pred eEEeccccccCC-CCceeeeechhhhhhhhcccCC---------ccccc--cccceeeeee
Confidence 356888987655 6778888999999999985432 12799 8987765543
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=94.07 E-value=0.033 Score=39.79 Aligned_cols=37 Identities=14% Similarity=0.515 Sum_probs=28.4
Q ss_pred CcccccccccCCCCCCceeeCCCC------ChhhHHHHHHHHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCS------HSYCTECMTKYVA 82 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~~ 82 (234)
...+|.||++.+...+.+...+|+ |.||.+|+++|-.
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 378999999999763444444675 7799999999953
No 68
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=93.85 E-value=0.034 Score=32.78 Aligned_cols=27 Identities=19% Similarity=0.449 Sum_probs=20.1
Q ss_pred CcccCCCCCc-eeeeccCCCceEec-CCCCC
Q 048114 206 NWRRCPNCKI-FVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 206 ~~k~CP~C~~-~i~k~~GCnhm~C~-C~~~F 234 (234)
..+.||+|+. .+.... +.++|. ||+++
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 4579999998 444444 799995 99864
No 69
>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=93.82 E-value=0.044 Score=29.68 Aligned_cols=27 Identities=22% Similarity=0.528 Sum_probs=17.1
Q ss_pred ccCCCCCceee-eccCCCceEec-CCCCC
Q 048114 208 RRCPNCKIFVE-KKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 208 k~CP~C~~~i~-k~~GCnhm~C~-C~~~F 234 (234)
+-||.|+.++. +.++=..+.|+ |+|++
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 57999999554 44444444995 99864
No 70
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.77 E-value=0.098 Score=44.14 Aligned_cols=56 Identities=21% Similarity=0.605 Sum_probs=41.0
Q ss_pred CcccccccccCCC--CCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114 46 TSFICDICVEPKS--TDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC 108 (234)
Q Consensus 46 ~~~~C~iC~~~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 108 (234)
-..+|+||++.+. .+.....+.|||.|=.+|+++|+. ....+.|| .|..+-....|
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp--~c~~katkr~i 60 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCP--LCSGKATKRQI 60 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCc--ccCChhHHHHH
Confidence 3568999999874 333444569999999999999993 33577899 78765444443
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.65 E-value=0.05 Score=29.86 Aligned_cols=31 Identities=26% Similarity=0.690 Sum_probs=23.1
Q ss_pred eecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 166 (234)
.+.|| .|+..+..+++ .....++|+.|+..|
T Consensus 2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 35799 99988877653 345579999998765
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.47 E-value=0.091 Score=48.31 Aligned_cols=55 Identities=25% Similarity=0.620 Sum_probs=43.6
Q ss_pred cCCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114 44 IETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK 100 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 100 (234)
....++|.||++.+.... +.+...|-|.|...|++.|....-.++...-+|| .|.
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cq 243 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQ 243 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--ccc
Confidence 466889999999986443 4566689999999999999998544456677999 676
No 73
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.11 E-value=0.025 Score=44.95 Aligned_cols=56 Identities=16% Similarity=0.431 Sum_probs=41.5
Q ss_pred cccccccccCCCCCC-------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114 47 SFICDICVEPKSTDE-------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 109 (234)
...|.||...+..+. ....++|+|.|.-.|++.|... | ..-.|| -|++.++....-
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----G-KkqtCP--YCKekVdl~rmf 286 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----G-KKQTCP--YCKEKVDLKRMF 286 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----c-CCCCCc--hHHHHhhHhhhc
Confidence 456999998875433 3334599999999999999853 3 245899 999988876543
No 74
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.05 E-value=0.052 Score=44.86 Aligned_cols=35 Identities=26% Similarity=0.585 Sum_probs=26.4
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA 82 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 82 (234)
.+...|+||+..-. . ..+.+|+|.-|.+|+.+|+-
T Consensus 420 sEd~lCpICyA~pi--~-Avf~PC~H~SC~~CI~qHlm 454 (489)
T KOG4692|consen 420 SEDNLCPICYAGPI--N-AVFAPCSHRSCYGCITQHLM 454 (489)
T ss_pred cccccCcceecccc--h-hhccCCCCchHHHHHHHHHh
Confidence 44668999987421 2 23459999999999999984
No 75
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.93 E-value=0.12 Score=40.64 Aligned_cols=57 Identities=14% Similarity=0.285 Sum_probs=44.0
Q ss_pred CCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 45 ETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
+..+.|+||-+.+...- ...+.+|||.||.+|++.+|. ..+.|| .++.++...+|-.
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~p--v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDP--VTDKPLKDRDIIG 276 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------cccccc--CCCCcCcccceEe
Confidence 56899999999986332 345779999999999999985 345678 7888887776543
No 76
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.27 E-value=0.083 Score=44.43 Aligned_cols=47 Identities=34% Similarity=0.844 Sum_probs=34.5
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK 100 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 100 (234)
....|-||-|.- +.+.+.+|||..|..|+..|-.+. + .-.||.+.|.
T Consensus 368 TFeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd--~---gq~CPFCRcE 414 (563)
T KOG1785|consen 368 TFELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSD--E---GQTCPFCRCE 414 (563)
T ss_pred hHHHHHHhhccC---CCcccccccchHHHHHHHhhcccC--C---CCCCCceeeE
Confidence 345799998753 667788999999999999887432 1 3468865553
No 77
>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=91.95 E-value=0.055 Score=42.28 Aligned_cols=52 Identities=19% Similarity=0.602 Sum_probs=37.1
Q ss_pred cccccccccCCCCCCcee---eCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFS---IKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~---~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...||||..+.-.+-.+. .+.|-|.+|-+|+.+.++ . .+-.||-.+|+.+|.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs----~--GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS----R--GPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc----C--CCCCCCCccHHHHHH
Confidence 346999997763322222 235999999999998885 2 367899999986544
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.91 E-value=0.13 Score=27.99 Aligned_cols=31 Identities=29% Similarity=0.633 Sum_probs=22.3
Q ss_pred eecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 166 (234)
.+.|| .|+..+..++. .....+.|+.|+..|
T Consensus 2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 35788 89988777643 344568999998764
No 79
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.68 E-value=0.16 Score=42.64 Aligned_cols=48 Identities=25% Similarity=0.705 Sum_probs=32.6
Q ss_pred cccccccccCCCCCCceeeC-CCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIK-GCSHSYCTECMTKYVASKLQENITSINCPVADCK 100 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 100 (234)
.-.|.||-+-++.+...... .|||.|...|+.+|+...-+ .-.|| .|+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps----~R~cp--ic~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS----NRGCP--ICQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCc----cCCCC--cee
Confidence 34699995555544444333 49999999999999964322 24688 665
No 80
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=91.66 E-value=0.17 Score=41.03 Aligned_cols=40 Identities=20% Similarity=0.551 Sum_probs=34.2
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASK 84 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~ 84 (234)
-+.-.|.||+--|..+..|....|.|+|...||.+|++..
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 4566899999888777778888999999999999999654
No 81
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=91.46 E-value=0.082 Score=45.15 Aligned_cols=49 Identities=22% Similarity=0.569 Sum_probs=35.4
Q ss_pred CCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
-+..+|+||+|....+- .+....|.|+|...|+..|. ...|| .|.....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---------~~scp--vcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---------DSSCP--VCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc---------cCcCh--hhhhhcC
Confidence 44679999999886432 33445999999999998876 45788 5654433
No 82
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.41 E-value=0.24 Score=40.12 Aligned_cols=44 Identities=23% Similarity=0.776 Sum_probs=33.3
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
+.|+.|.--+. +......|+|.||.+|+..-+.. ..+.|| .|..
T Consensus 275 LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d------sDf~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD------SDFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhhh--CcccCccccchHHHHHHhhhhhh------ccccCC--Cccc
Confidence 78999987654 55666789999999999876642 267899 6754
No 83
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=91.41 E-value=0.1 Score=29.36 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=20.6
Q ss_pred cCCcccCCCCCceeeeccCCCceEec---CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS---SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~F 234 (234)
..++++||+|+++- |+--+.|+ |++.|
T Consensus 8 lRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 8 LRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred HhccccCCcCcCcc----CcccccccCCccchhh
Confidence 46789999999975 66667784 77655
No 84
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.34 E-value=0.069 Score=31.57 Aligned_cols=44 Identities=27% Similarity=0.598 Sum_probs=31.1
Q ss_pred ccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGV 102 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 102 (234)
-+|.||+|.-. +.+ +-.|||. +|.+|-.+.++. ..=.|| .|..+
T Consensus 8 dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~~------~~g~CP--iCRap 52 (62)
T KOG4172|consen 8 DECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKKA------LHGCCP--ICRAP 52 (62)
T ss_pred cceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHHc------cCCcCc--chhhH
Confidence 56999998542 333 3489999 999999887753 233688 67654
No 85
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.77 E-value=0.25 Score=28.47 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=16.6
Q ss_pred ccCCCCCceeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
-.||+|+..++-.++=..++|. ||..
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCe
Confidence 4677888777654433367774 7764
No 86
>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=90.50 E-value=0.071 Score=31.45 Aligned_cols=37 Identities=27% Similarity=0.625 Sum_probs=17.5
Q ss_pred CCCCceecCCC--CccCcccCccccccccccCCCCCCCC
Q 048114 141 DCSALLIDDGG--EAIRESVCPDCNRMFCAQCKVPWHAG 177 (234)
Q Consensus 141 ~C~~~~~~~~~--~~~~~~~C~~C~~~~C~~C~~~~H~~ 177 (234)
+|...+..... .......|+.|+..||..|..-.|..
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 45554443321 11345899999999999887765643
No 87
>PF04641 Rtf2: Rtf2 RING-finger
Probab=90.42 E-value=0.37 Score=39.06 Aligned_cols=71 Identities=15% Similarity=0.358 Sum_probs=51.1
Q ss_pred cCCcccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCH-HHHHHHH
Q 048114 44 IETSFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPE-DVFNRWG 121 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~ 121 (234)
....+.|||...++... ..+.+.+|||.|...++++.- ..-.|| .|+..+...+|-.+-+. +.++.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--------~~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--------KSKKCP--VCGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--------cccccc--ccCCccccCCEEEecCCccHHHHHH
Confidence 36688999999998643 456677999999999998772 123499 99999998877666543 3444444
Q ss_pred HHH
Q 048114 122 NAL 124 (234)
Q Consensus 122 ~~~ 124 (234)
..+
T Consensus 180 ~~~ 182 (260)
T PF04641_consen 180 ERM 182 (260)
T ss_pred HHH
Confidence 333
No 88
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.93 E-value=0.092 Score=31.30 Aligned_cols=47 Identities=21% Similarity=0.458 Sum_probs=31.6
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
+...|-.|...-. . -.+++|+|.+|..|| .+..--.|| -|+..++..
T Consensus 6 ~~~~~~~~~~~~~--~-~~~~pCgH~I~~~~f---------~~~rYngCP--fC~~~~~~~ 52 (55)
T PF14447_consen 6 PEQPCVFCGFVGT--K-GTVLPCGHLICDNCF---------PGERYNGCP--FCGTPFEFD 52 (55)
T ss_pred cceeEEEcccccc--c-cccccccceeecccc---------ChhhccCCC--CCCCcccCC
Confidence 3455777755432 3 334699999999999 433344699 898887654
No 89
>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=89.89 E-value=0.12 Score=35.64 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=27.6
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMT 78 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~ 78 (234)
+++...|++|...+.. ..+...+|||.|...|++
T Consensus 75 i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 3567789999999865 556667999999999975
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=89.75 E-value=0.75 Score=37.24 Aligned_cols=51 Identities=22% Similarity=0.674 Sum_probs=35.2
Q ss_pred cccccccCCCCC--CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114 49 ICDICVEPKSTD--ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107 (234)
Q Consensus 49 ~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 107 (234)
.|++|-.+.-.. -...+-+|+|..|-+|+...+. ..+-.|| .|..++...-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~------~g~~~Cp--eC~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS------LGPAQCP--ECMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh------cCCCCCC--cccchhhhcc
Confidence 489998765322 1222349999999999988874 2355799 9988766543
No 91
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=89.37 E-value=0.096 Score=42.90 Aligned_cols=30 Identities=27% Similarity=0.463 Sum_probs=24.7
Q ss_pred CCcccCCCCCceeeecc-CCCceEec-CCCCC
Q 048114 205 ENWRRCPNCKIFVEKKE-GCRYMRCS-SNPQL 234 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~~-GCnhm~C~-C~~~F 234 (234)
..|.+||+|+..|.+.+ .=|.++|. |||||
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 45899999999888644 67889995 99997
No 92
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=89.25 E-value=0.43 Score=30.54 Aligned_cols=57 Identities=23% Similarity=0.482 Sum_probs=20.2
Q ss_pred CCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeeec
Q 048114 141 DCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKK 220 (234)
Q Consensus 141 ~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~ 220 (234)
-|+.-+-..... ...+.|..|+...|..| -+|.+ +...+-||+|+....+.
T Consensus 14 iCGD~VGl~~~G-e~FVAC~eC~fPvCr~C----------yEYEr------------------keg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 14 ICGDDVGLTENG-EVFVACHECAFPVCRPC----------YEYER------------------KEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp SS--B--B-SSS-SB--S-SSS-----HHH----------HHHHH------------------HTS-SB-TTT--B----
T ss_pred cccCccccCCCC-CEEEEEcccCCccchhH----------HHHHh------------------hcCcccccccCCCcccc
Confidence 565444333322 34488999999999844 44333 56779999999998887
Q ss_pred cCCCce
Q 048114 221 EGCRYM 226 (234)
Q Consensus 221 ~GCnhm 226 (234)
.|+..|
T Consensus 65 kgsp~V 70 (80)
T PF14569_consen 65 KGSPRV 70 (80)
T ss_dssp TT----
T ss_pred cCCCCC
Confidence 777543
No 93
>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=89.20 E-value=0.35 Score=25.42 Aligned_cols=27 Identities=22% Similarity=0.411 Sum_probs=17.6
Q ss_pred cccCCCCCceeeeccCCCceEec-CCCC
Q 048114 207 WRRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 207 ~k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
.+.||.|+.......|=--|.|. ||.+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 47899999999998887789995 8875
No 94
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.20 E-value=0.32 Score=28.65 Aligned_cols=28 Identities=36% Similarity=0.913 Sum_probs=19.6
Q ss_pred cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+|| .|+..+............|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 688 9998877765433345788888764
No 95
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.15 E-value=0.36 Score=42.27 Aligned_cols=40 Identities=30% Similarity=0.766 Sum_probs=28.4
Q ss_pred CeecCCCCCCCCceecCCCCccCcccCcc--ccccccccCCCCC--CC
Q 048114 133 QKFYCPFKDCSALLIDDGGEAIRESVCPD--CNRMFCAQCKVPW--HA 176 (234)
Q Consensus 133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~ 176 (234)
+...|| .|...+..+.. .+.+.|.. |++.||+.|...| |.
T Consensus 225 ntk~CP--~c~~~iek~~g--c~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 225 NTKECP--KCKVPIEKDGG--CNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred cCccCC--CcccchhccCC--ccccccccCCcCCeeceeeeccccccc
Confidence 334588 89888776543 33356655 9999999997776 64
No 96
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=89.09 E-value=0.23 Score=45.64 Aligned_cols=52 Identities=33% Similarity=0.829 Sum_probs=38.1
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
+.|.+|.+ . +.+.+..|+|.||.+|+...+... ....|| .|...+....+..
T Consensus 455 ~~c~ic~~---~-~~~~it~c~h~~c~~c~~~~i~~~-----~~~~~~--~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD---L-DSFFITRCGHDFCVECLKKSIQQS-----ENAPCP--LCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc---c-ccceeecccchHHHHHHHhccccc-----cCCCCc--HHHHHHHHHHHhh
Confidence 89999999 2 334445999999999999999533 223677 8887776665544
No 97
>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=88.71 E-value=0.17 Score=27.38 Aligned_cols=28 Identities=29% Similarity=0.743 Sum_probs=19.1
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.+|| .|++.+....+..... .|+.|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 4789 9999988776554443 78888764
No 98
>PHA03096 p28-like protein; Provisional
Probab=88.66 E-value=0.3 Score=39.92 Aligned_cols=39 Identities=21% Similarity=0.401 Sum_probs=30.6
Q ss_pred ccccccccCCCCC-----CceeeCCCCChhhHHHHHHHHHHHHh
Q 048114 48 FICDICVEPKSTD-----ESFSIKGCSHSYCTECMTKYVASKLQ 86 (234)
Q Consensus 48 ~~C~iC~~~~~~~-----~~~~~~~C~H~fC~~Cl~~~~~~~i~ 86 (234)
..|.||++..... ..-.+..|.|.||..|++.|......
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 7899999987532 12235699999999999999987753
No 99
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=88.54 E-value=0.32 Score=28.21 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=19.2
Q ss_pred CCcccCCCCCceeeeccCCCceEe-cCCCC
Q 048114 205 ENWRRCPNCKIFVEKKEGCRYMRC-SSNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~ 233 (234)
...+.||+|+--+....-=+...| +|||.
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccce
Confidence 345799999964444333348889 69873
No 100
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.09 E-value=0.4 Score=25.71 Aligned_cols=25 Identities=20% Similarity=0.545 Sum_probs=14.1
Q ss_pred ccCCCCCceeeec----cCCCceEec-CCC
Q 048114 208 RRCPNCKIFVEKK----EGCRYMRCS-SNP 232 (234)
Q Consensus 208 k~CP~C~~~i~k~----~GCnhm~C~-C~~ 232 (234)
|.||.|+..++.. ++=..+.|. ||+
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 5799999988862 567779995 885
No 101
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.13 E-value=0.42 Score=44.46 Aligned_cols=41 Identities=29% Similarity=0.614 Sum_probs=34.0
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKL 85 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 85 (234)
+++...|.+|.-.+.. ++|.+.+|||.|.++|+.+++....
T Consensus 814 ~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred ecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHHccc
Confidence 4778899999988854 5677779999999999999986543
No 102
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.84 E-value=0.48 Score=38.18 Aligned_cols=54 Identities=19% Similarity=0.516 Sum_probs=39.7
Q ss_pred CCcccccccccCCCCCCceeeCCC-CChhhHHHHHHHHHHHHhcCCccccCCCC-CCC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGC-SHSYCTECMTKYVASKLQENITSINCPVA-DCK 100 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~-~C~ 100 (234)
...+-|.+|.|.++...+++..+= .|.||.-|-++.|+.+-. ...+.||.. .|.
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~--sgevYCPSGdkCP 321 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGA--SGEVYCPSGDKCP 321 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcC--CCceeCCCCCcCc
Confidence 445899999999976665543221 799999999999988743 347899963 454
No 103
>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=86.79 E-value=0.37 Score=26.36 Aligned_cols=30 Identities=17% Similarity=0.506 Sum_probs=20.3
Q ss_pred ecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114 135 FYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF 166 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 166 (234)
+.|| .|+..+..+.+ .....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688 89987766532 123358999998764
No 104
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.23 E-value=0.41 Score=23.17 Aligned_cols=22 Identities=45% Similarity=1.224 Sum_probs=14.1
Q ss_pred cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+|| .|+..+..+ ..+|+.||+.
T Consensus 1 ~Cp--~CG~~~~~~------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDD------AKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCc------CcchhhhCCc
Confidence 477 788766422 2568888764
No 105
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.14 E-value=1.4 Score=39.59 Aligned_cols=59 Identities=17% Similarity=0.472 Sum_probs=36.4
Q ss_pred CccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 89 ITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 89 ~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
...+.|| .|...+....+..++. .=....+.||..+|+..+..... ...+.|+.|+..|
T Consensus 405 ~~~V~C~--NC~~~i~l~~l~lHe~---------------~C~r~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f 463 (567)
T PLN03086 405 VDTVECR--NCKHYIPSRSIALHEA---------------YCSRHNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF 463 (567)
T ss_pred CCeEECC--CCCCccchhHHHHHHh---------------hCCCcceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence 4567899 5988877666542210 01123456887679988765433 2346888887765
No 106
>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=86.08 E-value=0.79 Score=25.70 Aligned_cols=23 Identities=26% Similarity=0.692 Sum_probs=18.1
Q ss_pred cccCCCCCceeee-ccCCCceEec-CC
Q 048114 207 WRRCPNCKIFVEK-KEGCRYMRCS-SN 231 (234)
Q Consensus 207 ~k~CP~C~~~i~k-~~GCnhm~C~-C~ 231 (234)
...||.|+.++.+ .+| .+.|. |+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3799999998888 556 68885 74
No 107
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=85.88 E-value=1.4 Score=36.47 Aligned_cols=55 Identities=25% Similarity=0.600 Sum_probs=37.9
Q ss_pred cccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114 47 SFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109 (234)
Q Consensus 47 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 109 (234)
.-.|++|++++... +.|.-.+||-.+|+-||...- ++ ..=+|| .|....+.+.++
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~ir-----q~-lngrcp--acrr~y~denv~ 69 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIR-----QN-LNGRCP--ACRRKYDDENVR 69 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHH-----hh-ccCCCh--Hhhhhcccccee
Confidence 44599999998643 334344889999999995432 33 234799 898887776555
No 108
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=85.34 E-value=0.37 Score=40.58 Aligned_cols=50 Identities=28% Similarity=0.697 Sum_probs=37.7
Q ss_pred CCcccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
+-.+.|..|.+-+... +....++|.|+|...|+..++. +..+-.|| .|..
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~-----~n~~rsCP--~Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE-----NNGTRSCP--NCRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH-----hCCCCCCc--cHHH
Confidence 4467899999988432 3445679999999999999983 33466899 7763
No 109
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=84.63 E-value=0.74 Score=38.00 Aligned_cols=46 Identities=28% Similarity=0.592 Sum_probs=32.6
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...++||||++.+...- ++ .+=||..|.+|-. ...-+|| .|...+.
T Consensus 46 ~~lleCPvC~~~l~~Pi-~Q-C~nGHlaCssC~~----------~~~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPI-FQ-CDNGHLACSSCRT----------KVSNKCP--TCRLPIG 91 (299)
T ss_pred hhhccCchhhccCcccc-ee-cCCCcEehhhhhh----------hhcccCC--ccccccc
Confidence 44788999999985211 22 1448999999985 1345899 6887777
No 110
>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=84.26 E-value=1.2 Score=22.72 Aligned_cols=21 Identities=33% Similarity=0.751 Sum_probs=13.9
Q ss_pred cCCCCCceeeeccCCCceEec
Q 048114 209 RCPNCKIFVEKKEGCRYMRCS 229 (234)
Q Consensus 209 ~CP~C~~~i~k~~GCnhm~C~ 229 (234)
.||.|+..+.+.+|=-...|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 599999999999887788874
No 111
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=84.06 E-value=0.62 Score=43.56 Aligned_cols=24 Identities=33% Similarity=0.858 Sum_probs=21.3
Q ss_pred ccCCCCCceeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
..||.|+..+...+||. +|+ |||.
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCC
Confidence 36999999999999998 996 9984
No 112
>PF12773 DZR: Double zinc ribbon
Probab=84.03 E-value=0.9 Score=26.46 Aligned_cols=26 Identities=27% Similarity=0.844 Sum_probs=12.7
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+|| .|+..+.. .....+.|+.|++
T Consensus 12 ~~fC~--~CG~~l~~---~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCP--HCGTPLPP---PDQSKKICPNCGA 37 (50)
T ss_pred ccCCh--hhcCChhh---ccCCCCCCcCCcC
Confidence 34666 66665541 1122255665544
No 113
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=83.98 E-value=0.65 Score=33.14 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=21.4
Q ss_pred CcccCCCCCceeeeccCCCceEec-CCCC
Q 048114 206 NWRRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 206 ~~k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
..+.||.||.+.++.+| .++|. ||+.
T Consensus 27 L~~hCp~Cg~PLF~KdG--~v~CPvC~~~ 53 (131)
T COG1645 27 LAKHCPKCGTPLFRKDG--EVFCPVCGYR 53 (131)
T ss_pred HHhhCcccCCcceeeCC--eEECCCCCce
Confidence 34899999999998776 79994 9864
No 114
>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=83.72 E-value=0.97 Score=26.12 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=20.3
Q ss_pred CcccCC--CCCceeeeccCCCceEe-cCCC
Q 048114 206 NWRRCP--NCKIFVEKKEGCRYMRC-SSNP 232 (234)
Q Consensus 206 ~~k~CP--~C~~~i~k~~GCnhm~C-~C~~ 232 (234)
.-+.|| +|+.-+.-..--+..+| +||+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 358999 99997777666789999 6986
No 115
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=83.68 E-value=0.15 Score=41.72 Aligned_cols=82 Identities=21% Similarity=0.491 Sum_probs=44.5
Q ss_pred hhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHH----H--HhCCCeecCCCCCCCC
Q 048114 71 SYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEA----V--ILGAQKFYCPFKDCSA 144 (234)
Q Consensus 71 ~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~----~--~~~~~~~~Cp~~~C~~ 144 (234)
.||..|-..+.. .|+.|| .|...| ++++.+...|..+.--. . ........|- .|+.
T Consensus 277 y~CP~CkakvCs-------LP~eCp--iC~ltL-------Vss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~ 338 (378)
T KOG2807|consen 277 YFCPQCKAKVCS-------LPIECP--ICSLTL-------VSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQG 338 (378)
T ss_pred eeCCcccCeeec-------CCccCC--ccceeE-------ecchHHHHHHHhhcCCcchhhccccccCCCccee--eecc
Confidence 455555443332 678888 675432 23344444454443111 0 1122334576 6632
Q ss_pred ceecCCCCccCcccCccccccccccCCCCCC
Q 048114 145 LLIDDGGEAIRESVCPDCNRMFCAQCKVPWH 175 (234)
Q Consensus 145 ~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H 175 (234)
. .......+|..|+..||..|..-.|
T Consensus 339 ~-----~~~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 339 E-----LLSSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred c-----cCCCCcEEchhccceeeccchHHHH
Confidence 2 2223448999999999999977555
No 116
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.59 E-value=0.62 Score=23.21 Aligned_cols=23 Identities=30% Similarity=1.003 Sum_probs=14.4
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+.|| .|+..+.. + ..+|+.||+.
T Consensus 3 ~~Cp--~Cg~~~~~-~-----~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDP-D-----AKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCc-c-----cccChhhCCC
Confidence 4688 88874322 1 2678888764
No 117
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.57 E-value=0.36 Score=39.11 Aligned_cols=33 Identities=27% Similarity=0.571 Sum_probs=26.9
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA 82 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 82 (234)
.+-|.||-.++. +++. ..|+|+||..|....++
T Consensus 241 Pf~c~icr~~f~--~pVv-t~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVV-TKCGHYFCEVCALKPYQ 273 (313)
T ss_pred Cccccccccccc--cchh-hcCCceeehhhhccccc
Confidence 567999999985 4454 59999999999977764
No 118
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=83.53 E-value=1.2 Score=43.33 Aligned_cols=29 Identities=31% Similarity=0.903 Sum_probs=21.1
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccc-----cccCCCC
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMF-----CAQCKVP 173 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~ 173 (234)
+.|| .|+..... .+|+.||... |..|+..
T Consensus 668 rkCP--kCG~~t~~--------~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCP--SCGTETYE--------NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECC--CCCCcccc--------ccCcccCCcCCCceeCccCCCc
Confidence 6899 89875321 4899998775 8888774
No 119
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=82.92 E-value=1.6 Score=26.00 Aligned_cols=33 Identities=21% Similarity=0.528 Sum_probs=27.5
Q ss_pred cccccccccCCC-CCCceeeCCCCChhhHHHHHH
Q 048114 47 SFICDICVEPKS-TDESFSIKGCSHSYCTECMTK 79 (234)
Q Consensus 47 ~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~ 79 (234)
.-.|++|.+.|. .++.+....|+-.+.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999996 556777789999999999964
No 120
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.64 E-value=1.4 Score=26.68 Aligned_cols=32 Identities=19% Similarity=0.575 Sum_probs=20.8
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCC
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCK 171 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 171 (234)
.|. +|+..+...+ ....+.||.||...=++|.
T Consensus 11 ~Ct--SCg~~i~p~e--~~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 11 VCT--SCGREIAPGE--TAVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred eec--cCCCEeccCC--ceeEeeCCCCCceeeehhh
Confidence 566 7877764332 2345899999977666554
No 121
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.62 E-value=0.86 Score=41.77 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=8.7
Q ss_pred CCcccCCCCCceee
Q 048114 205 ENWRRCPNCKIFVE 218 (234)
Q Consensus 205 ~~~k~CP~C~~~i~ 218 (234)
.+.+.||+||....
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 34567777776543
No 122
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=82.53 E-value=0.98 Score=36.66 Aligned_cols=46 Identities=28% Similarity=0.649 Sum_probs=34.6
Q ss_pred cccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 47 SFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 47 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
...||||.+.+... ..+..++|||..-..|++.++. ++ .+|| .|..
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~---y~CP--~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG---YTCP--ICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC---CCCC--cccc
Confidence 44599999987433 3344569999999999998884 22 7899 7876
No 123
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=81.47 E-value=2.4 Score=27.89 Aligned_cols=31 Identities=16% Similarity=0.382 Sum_probs=26.3
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
......||.|+....|..+=---.|. ||+.|
T Consensus 32 ~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 32 QRAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HhcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 45567999999999998888888995 99987
No 124
>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=81.17 E-value=1.4 Score=26.12 Aligned_cols=27 Identities=19% Similarity=0.255 Sum_probs=18.2
Q ss_pred cccCCCCCceee------eccCCCceE-ec-CCCC
Q 048114 207 WRRCPNCKIFVE------KKEGCRYMR-CS-SNPQ 233 (234)
Q Consensus 207 ~k~CP~C~~~i~------k~~GCnhm~-C~-C~~~ 233 (234)
.|+||-|+-.-+ .+.+..++. |. ||++
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 379999998444 233566664 85 9875
No 125
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=81.15 E-value=1.1 Score=25.96 Aligned_cols=33 Identities=24% Similarity=0.693 Sum_probs=21.8
Q ss_pred ccccccCCCCCCceeeCCCCC-----hhhHHHHHHHHHH
Q 048114 50 CDICVEPKSTDESFSIKGCSH-----SYCTECMTKYVAS 83 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~ 83 (234)
|-||++....+.... .+|.. .+..+||.+|+..
T Consensus 1 CrIC~~~~~~~~~li-~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLI-SPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE--SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCcee-cccccCCCcchhHHHHHHHHHHh
Confidence 668998876555333 46743 4789999999987
No 126
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=80.28 E-value=1.9 Score=24.33 Aligned_cols=24 Identities=21% Similarity=0.459 Sum_probs=13.7
Q ss_pred cCCCCCce-eeeccCCCceEec-CCC
Q 048114 209 RCPNCKIF-VEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 209 ~CP~C~~~-i~k~~GCnhm~C~-C~~ 232 (234)
.||.|+.. +.-+..=..+.|. ||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 47777773 3444555566774 764
No 127
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.97 E-value=2.3 Score=25.78 Aligned_cols=31 Identities=19% Similarity=0.660 Sum_probs=19.6
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccC
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQC 170 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C 170 (234)
.|. .|+..+...+ ....+.||.||...=++|
T Consensus 9 ~Ct--SCg~~i~~~~--~~~~F~CPnCG~~~I~RC 39 (59)
T PRK14890 9 KCT--SCGIEIAPRE--KAVKFLCPNCGEVIIYRC 39 (59)
T ss_pred ccc--CCCCcccCCC--ccCEeeCCCCCCeeEeec
Confidence 466 7777665333 245589999988744444
No 128
>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=79.59 E-value=1.2 Score=25.18 Aligned_cols=41 Identities=24% Similarity=0.687 Sum_probs=18.5
Q ss_pred ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
|.+|.+-......=....|+-.+...|++.|+... ..-+||
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~-----~~~~CP 41 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR-----SNPKCP 41 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT------SS-B-T
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC-----CCCCCc
Confidence 56676655422211122688889999999999643 222788
No 129
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.39 E-value=0.78 Score=43.19 Aligned_cols=57 Identities=26% Similarity=0.574 Sum_probs=40.0
Q ss_pred hhhcCCcccccccccCCCC-CC-c--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 41 EERIETSFICDICVEPKST-DE-S--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 41 ~~~~~~~~~C~iC~~~~~~-~~-~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...++...+|.||+..+.. +. . -....|.|.|...|+-+|+.+. ..-+|| -|+..++
T Consensus 1463 ~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss-----~~s~CP--lCRseit 1523 (1525)
T COG5219 1463 DEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS-----ARSNCP--LCRSEIT 1523 (1525)
T ss_pred hhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc-----CCCCCC--ccccccc
Confidence 4446777899999987641 11 1 1234799999999999999754 344799 7876554
No 130
>PRK00420 hypothetical protein; Validated
Probab=79.06 E-value=1.6 Score=30.38 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=20.7
Q ss_pred CcccCCCCCceeee-ccCCCceEec-CCC
Q 048114 206 NWRRCPNCKIFVEK-KEGCRYMRCS-SNP 232 (234)
Q Consensus 206 ~~k~CP~C~~~i~k-~~GCnhm~C~-C~~ 232 (234)
....||.|+.+..+ .+| +..|. ||.
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCCC
Confidence 44899999999998 666 88995 886
No 131
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=78.82 E-value=5 Score=37.44 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=7.7
Q ss_pred cccCCCCCce
Q 048114 207 WRRCPNCKIF 216 (234)
Q Consensus 207 ~k~CP~C~~~ 216 (234)
...||+|+..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 4688888876
No 132
>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=78.81 E-value=1.2 Score=28.08 Aligned_cols=24 Identities=21% Similarity=0.549 Sum_probs=14.6
Q ss_pred cCCCCCceeeeccCCCceEec-CCCCC
Q 048114 209 RCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 209 ~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
.||.|+..++..+ .+.+|. |+.+|
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~ 27 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDY 27 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EE
T ss_pred cCCCCCCccEEeC--CEEECccccccc
Confidence 5888888887777 677774 76654
No 133
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.14 E-value=2 Score=29.91 Aligned_cols=41 Identities=24% Similarity=0.598 Sum_probs=28.1
Q ss_pred ecCCCCCCCCceecCCC------CccCcccCccccccccccCCCCCCCC
Q 048114 135 FYCPFKDCSALLIDDGG------EAIRESVCPDCNRMFCAQCKVPWHAG 177 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~------~~~~~~~C~~C~~~~C~~C~~~~H~~ 177 (234)
..|- +|...+..... .......|+.|+..||..|..-+|..
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 4577 88876653211 12234789999999999998877743
No 134
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.29 E-value=3 Score=32.60 Aligned_cols=54 Identities=19% Similarity=0.503 Sum_probs=40.5
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhc-CCccccCCCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQE-NITSINCPVADCKGVL 103 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~l 103 (234)
.-.|.+|...+...+.+.+ .|-|.|..+|+..+...--.. .-...+|| .|...+
T Consensus 50 ~pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP--~Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCP--CCSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCC--CCCCcc
Confidence 4569999999988787776 999999999999887543222 23457899 776544
No 135
>PRK04023 DNA polymerase II large subunit; Validated
Probab=76.35 E-value=2.2 Score=40.66 Aligned_cols=29 Identities=28% Similarity=0.722 Sum_probs=18.3
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccc-----cccccCCCC
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNR-----MFCAQCKVP 173 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~ 173 (234)
+.|| .|+... ....|+.||. .+|..|+..
T Consensus 627 RfCp--sCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 627 RKCP--SCGKET--------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCC--CCCCcC--------CcccCCCCCCCCCcceeCccccCc
Confidence 4777 777653 2267777874 467777553
No 136
>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=76.35 E-value=2.7 Score=24.64 Aligned_cols=47 Identities=19% Similarity=0.509 Sum_probs=24.9
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
+.|+|-+..+. -++....|.|.-|.| +..|+......+ ..+|| .|.+
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~--~W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTP--KWKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS-----B-T--TT--
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccC--CeECc--CCcC
Confidence 56888887765 567778999998755 567776665443 37899 6754
No 137
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.04 E-value=0.95 Score=33.35 Aligned_cols=29 Identities=21% Similarity=0.409 Sum_probs=23.8
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhh
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYC 73 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC 73 (234)
+..-+|.||+|++...+.+..++|-.+|.
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEee
Confidence 55678999999998888888889977664
No 138
>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=76.03 E-value=1.5 Score=27.47 Aligned_cols=28 Identities=21% Similarity=0.500 Sum_probs=22.2
Q ss_pred CcccCCCCCceeeeccCCCceEec-CCCC
Q 048114 206 NWRRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 206 ~~k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
..+.||.|+....+...=-.++|. ||++
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 458999999999885555578896 9875
No 139
>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=75.92 E-value=2.8 Score=25.08 Aligned_cols=30 Identities=30% Similarity=0.663 Sum_probs=22.7
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
+.|| .|+..+..........+.|+.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 3688 89998877655556678999998765
No 140
>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=75.71 E-value=2.4 Score=25.19 Aligned_cols=40 Identities=20% Similarity=0.476 Sum_probs=23.2
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
.+.||.|...++. .=|..++...=..+...+.|| .|...+
T Consensus 2 ~f~CP~C~~~~~~---------------~~L~~H~~~~H~~~~~~v~CP--iC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSE---------------SSLVEHCEDEHRSESKNVVCP--ICSSRV 41 (54)
T ss_pred CcCCCCCCCccCH---------------HHHHHHHHhHCcCCCCCccCC--Cchhhh
Confidence 6789999885431 123444443322334578999 787543
No 141
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.52 E-value=0.77 Score=42.26 Aligned_cols=42 Identities=17% Similarity=0.249 Sum_probs=22.2
Q ss_pred CCcccccccccCCCC-CCceeeC---CCCChhhHHHHHHHHHHHHh
Q 048114 45 ETSFICDICVEPKST-DESFSIK---GCSHSYCTECMTKYVASKLQ 86 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~-~~~~~~~---~C~H~fC~~Cl~~~~~~~i~ 86 (234)
.+..+|.+|..++.. .+.+... .|+|.+|..||..+....+.
T Consensus 94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 335556666555542 1112222 36777777777776655543
No 142
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=75.04 E-value=3.2 Score=22.04 Aligned_cols=28 Identities=14% Similarity=0.321 Sum_probs=17.3
Q ss_pred cccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 207 WRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 207 ~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
.+.|+.|+....-+.-=..+.|. ||..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 46788888843332333478885 87654
No 143
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=74.48 E-value=3.4 Score=25.04 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=20.4
Q ss_pred ccCCCCCc----eeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKI----FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~----~i~k~~GCnhm~C~-C~~~ 233 (234)
..||+|+. ++.+..|=.++.|. |||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 58999987 34467777899996 9985
No 144
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=74.15 E-value=2.5 Score=40.75 Aligned_cols=60 Identities=22% Similarity=0.514 Sum_probs=40.7
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~ 215 (234)
-|. -|+.-+-...+. ..-+.|..|+...|..| -+|++ +.+.+-||.|+.
T Consensus 19 iCq--ICGD~vg~~~~G-e~FVAC~eC~FPVCrpC----------YEYEr------------------~eG~q~CPqCkt 67 (1079)
T PLN02638 19 VCQ--ICGDNVGKTVDG-EPFVACDVCAFPVCRPC----------YEYER------------------KDGNQSCPQCKT 67 (1079)
T ss_pred eee--ecccccCcCCCC-CEEEEeccCCCccccch----------hhhhh------------------hcCCccCCccCC
Confidence 355 566554443322 34589999999999855 44433 456789999999
Q ss_pred eeeeccCCCce
Q 048114 216 FVEKKEGCRYM 226 (234)
Q Consensus 216 ~i~k~~GCnhm 226 (234)
...+--|++.+
T Consensus 68 rYkr~kgsprv 78 (1079)
T PLN02638 68 KYKRHKGSPAI 78 (1079)
T ss_pred chhhhcCCCCc
Confidence 88877777654
No 145
>PRK14873 primosome assembly protein PriA; Provisional
Probab=73.63 E-value=7.6 Score=36.00 Aligned_cols=18 Identities=22% Similarity=0.683 Sum_probs=9.8
Q ss_pred CcccCccccc-cccccCCC
Q 048114 155 RESVCPDCNR-MFCAQCKV 172 (234)
Q Consensus 155 ~~~~C~~C~~-~~C~~C~~ 172 (234)
+.+.|..||. ..|.+|..
T Consensus 382 p~l~C~~Cg~~~~C~~C~~ 400 (665)
T PRK14873 382 PSLACARCRTPARCRHCTG 400 (665)
T ss_pred CeeEhhhCcCeeECCCCCC
Confidence 4456666653 34566654
No 146
>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=72.66 E-value=2.3 Score=35.18 Aligned_cols=53 Identities=19% Similarity=0.420 Sum_probs=31.9
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~ 215 (234)
.|| .|.......+... ..+. .||+.||..|.... . ..+..+||.|+.
T Consensus 5 ~CP--~Ck~~~y~np~~k-l~i~--~CGH~~C~sCv~~l---------------------------~-~~~~~~CP~C~~ 51 (309)
T TIGR00570 5 GCP--RCKTTKYRNPSLK-LMVN--VCGHTLCESCVDLL---------------------------F-VRGSGSCPECDT 51 (309)
T ss_pred CCC--cCCCCCccCcccc-cccC--CCCCcccHHHHHHH---------------------------h-cCCCCCCCCCCC
Confidence 588 7886443333221 1123 79999999885420 1 123358999998
Q ss_pred eeeecc
Q 048114 216 FVEKKE 221 (234)
Q Consensus 216 ~i~k~~ 221 (234)
.+.|+.
T Consensus 52 ~lrk~~ 57 (309)
T TIGR00570 52 PLRKNN 57 (309)
T ss_pred ccchhh
Confidence 887753
No 147
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=71.48 E-value=2.6 Score=28.33 Aligned_cols=29 Identities=31% Similarity=0.883 Sum_probs=20.8
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.+|| .|++.++...+...+.+.|..|.+.
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 3689 9999888877665556667666554
No 148
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=71.24 E-value=2.7 Score=29.40 Aligned_cols=30 Identities=27% Similarity=0.618 Sum_probs=22.6
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.+|| .|++.+.+..+.....+.|++|++..
T Consensus 3 ~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 5799 99999888654444568888888764
No 149
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=71.11 E-value=3.9 Score=27.82 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=21.0
Q ss_pred CCcccCCCCCcee---eeccCCCceEec-CCCCC
Q 048114 205 ENWRRCPNCKIFV---EKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 205 ~~~k~CP~C~~~i---~k~~GCnhm~C~-C~~~F 234 (234)
...-.||+|+... .+..|=.|.+|. ||+-|
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 4557899999432 234477799995 99854
No 150
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.68 E-value=0.94 Score=34.03 Aligned_cols=31 Identities=29% Similarity=0.835 Sum_probs=21.9
Q ss_pred ccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeee
Q 048114 160 PDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEK 219 (234)
Q Consensus 160 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k 219 (234)
.+||+.||..|.+. . .....+||-|+..|.+
T Consensus 149 TkCGHvFC~~Cik~-----------------------a------lk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKD-----------------------A------LKNTNKCPTCRKKITH 179 (187)
T ss_pred cccchhHHHHHHHH-----------------------H------HHhCCCCCCcccccch
Confidence 47999999988541 1 1346799999976653
No 151
>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=70.59 E-value=4.5 Score=25.06 Aligned_cols=17 Identities=24% Similarity=0.841 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHHHHhcC
Q 048114 72 YCTECMTKYVASKLQEN 88 (234)
Q Consensus 72 fC~~Cl~~~~~~~i~~~ 88 (234)
||+.||.+|+.....+.
T Consensus 12 FCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 12 FCRNCLSKWYREAAEER 28 (68)
T ss_dssp --HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999999887653
No 152
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=70.57 E-value=4.3 Score=33.44 Aligned_cols=58 Identities=22% Similarity=0.457 Sum_probs=41.9
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 107 (234)
+-+-+.||+=-+.-...+++..+.|||.+=.+=+...- ++|...++|| .|+..-..+.
T Consensus 333 fHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~~~FKCP--YCP~~~~~~~ 390 (396)
T COG5109 333 FHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGVLSFKCP--YCPEMSKYEN 390 (396)
T ss_pred ccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCcEEeeCC--CCCcchhhhh
Confidence 45678999977777666788888999998665554332 3577899999 8986544443
No 153
>PRK00420 hypothetical protein; Validated
Probab=70.49 E-value=12 Score=26.14 Aligned_cols=26 Identities=31% Similarity=0.595 Sum_probs=17.3
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
..|| .|+..++.... ...+||.||..
T Consensus 24 ~~CP--~Cg~pLf~lk~---g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCP--VCGLPLFELKD---GEVVCPVHGKV 49 (112)
T ss_pred CCCC--CCCCcceecCC---CceECCCCCCe
Confidence 5799 89987776322 12778777664
No 154
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=70.13 E-value=6.5 Score=31.43 Aligned_cols=21 Identities=19% Similarity=0.507 Sum_probs=16.0
Q ss_pred CCCeecCCCCCCCCceecCCC
Q 048114 131 GAQKFYCPFKDCSALLIDDGG 151 (234)
Q Consensus 131 ~~~~~~Cp~~~C~~~~~~~~~ 151 (234)
....+.||+++|..++.....
T Consensus 120 sS~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 120 SSQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred ccccccCCCCCCcceEEeCCc
Confidence 345678999999998876543
No 155
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=69.85 E-value=4.4 Score=25.76 Aligned_cols=26 Identities=23% Similarity=0.742 Sum_probs=20.7
Q ss_pred ccCCCCCc----eeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKI----FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~----~i~k~~GCnhm~C~-C~~~ 233 (234)
..||+|+. ++.+..|=.++.|. |||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 48999987 34467788899995 9986
No 156
>PLN02189 cellulose synthase
Probab=69.81 E-value=3.9 Score=39.34 Aligned_cols=60 Identities=22% Similarity=0.504 Sum_probs=41.2
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~ 215 (234)
-|. -|+..+-.+... ..-+.|..|+...|..|. +|.+ +...+.||.|+.
T Consensus 36 ~C~--iCgd~vg~~~~g-~~fvaC~~C~fpvCr~Cy----------eyer------------------~eg~q~CpqCkt 84 (1040)
T PLN02189 36 VCE--ICGDEIGLTVDG-DLFVACNECGFPVCRPCY----------EYER------------------REGTQNCPQCKT 84 (1040)
T ss_pred ccc--ccccccCcCCCC-CEEEeeccCCCccccchh----------hhhh------------------hcCCccCcccCC
Confidence 566 677665544333 345899999999998664 3322 456689999999
Q ss_pred eeeeccCCCce
Q 048114 216 FVEKKEGCRYM 226 (234)
Q Consensus 216 ~i~k~~GCnhm 226 (234)
...+--|++.+
T Consensus 85 ~Y~r~kgs~~v 95 (1040)
T PLN02189 85 RYKRLKGSPRV 95 (1040)
T ss_pred chhhccCCCCc
Confidence 88876676654
No 157
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=68.66 E-value=8.5 Score=28.50 Aligned_cols=51 Identities=18% Similarity=0.414 Sum_probs=35.6
Q ss_pred CCcccccccccCCCCCCceeeCCCCC-----hhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSH-----SYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
.....|=||+++-. ... .+|.. ....+|+++|+... ....|+ .|...+...
T Consensus 6 ~~~~~CRIC~~~~~--~~~--~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Ce--iC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYD--VVT--NYCNCKNENKIVHKECLEEWINTS-----KNKSCK--ICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCC--Ccc--CCcccCCCchHHHHHHHHHHHhcC-----CCCccc--ccCCeEEEE
Confidence 34667999998854 222 25544 47999999999743 467899 888766554
No 158
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=68.60 E-value=5.3 Score=24.23 Aligned_cols=27 Identities=22% Similarity=0.671 Sum_probs=17.1
Q ss_pred CcccCCCCCceee--ecc-C--C---CceEec-CCC
Q 048114 206 NWRRCPNCKIFVE--KKE-G--C---RYMRCS-SNP 232 (234)
Q Consensus 206 ~~k~CP~C~~~i~--k~~-G--C---nhm~C~-C~~ 232 (234)
.+|+||-||.... +.. + - -.|.|. ||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4689999996332 222 2 1 468896 886
No 159
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=68.12 E-value=5.3 Score=24.66 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=18.7
Q ss_pred CCcccCCCCCceeee---ccCCCceEe-cCCC
Q 048114 205 ENWRRCPNCKIFVEK---KEGCRYMRC-SSNP 232 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k---~~GCnhm~C-~C~~ 232 (234)
..+|+||-|+..+.+ .+|=-...| +|+.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 457999999985443 455445677 4875
No 160
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.37 E-value=11 Score=31.51 Aligned_cols=33 Identities=24% Similarity=0.639 Sum_probs=26.1
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKY 80 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 80 (234)
++...|.||.+.+ .-..+++|+|..|.-|..+.
T Consensus 59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~Rl 91 (493)
T COG5236 59 EENMNCQICAGST---TYSARYPCGHQICHACAVRL 91 (493)
T ss_pred cccceeEEecCCc---eEEEeccCCchHHHHHHHHH
Confidence 5577899998866 34567799999999998654
No 161
>PF14149 YhfH: YhfH-like protein
Probab=67.20 E-value=0.64 Score=25.30 Aligned_cols=28 Identities=18% Similarity=0.472 Sum_probs=20.9
Q ss_pred HHhcCCcccCCCCCceeeeccCCCceEe
Q 048114 201 LAQKENWRRCPNCKIFVEKKEGCRYMRC 228 (234)
Q Consensus 201 ~~~~~~~k~CP~C~~~i~k~~GCnhm~C 228 (234)
+......|.|+.||..|+-..-|-.++|
T Consensus 7 FfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 3446678999999999887666666666
No 162
>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=67.10 E-value=3.1 Score=21.31 Aligned_cols=24 Identities=25% Similarity=0.706 Sum_probs=13.4
Q ss_pred ccCCCCCceeee--ccCCCceEe-cCC
Q 048114 208 RRCPNCKIFVEK--KEGCRYMRC-SSN 231 (234)
Q Consensus 208 k~CP~C~~~i~k--~~GCnhm~C-~C~ 231 (234)
++||+|+..|++ .+|=+...| +|.
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 589999999976 345555666 354
No 163
>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=66.85 E-value=2.8 Score=22.59 Aligned_cols=25 Identities=24% Similarity=0.648 Sum_probs=20.6
Q ss_pred CcccCccccccccccCCCCCCCCCC
Q 048114 155 RESVCPDCNRMFCAQCKVPWHAGIR 179 (234)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~H~~~~ 179 (234)
..++|..|+..+|..|....|.++.
T Consensus 11 ~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 11 LSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred eEEEeCccChhhhhhcChhhcCCCC
Confidence 3589999999999999876687654
No 164
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=66.15 E-value=2.9 Score=39.51 Aligned_cols=24 Identities=38% Similarity=0.920 Sum_probs=20.6
Q ss_pred ccCCCCCc-eeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKI-FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~-~i~k~~GCnhm~C~-C~~~ 233 (234)
-.||-|+. .|+..|||| ||. ||++
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999999 888999999 785 8765
No 165
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=65.39 E-value=6.6 Score=23.13 Aligned_cols=30 Identities=27% Similarity=0.577 Sum_probs=22.5
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHH
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKY 80 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 80 (234)
.|.||.+++..-..+.+ .=| .+|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 49999998865444444 556 7999999876
No 166
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.16 E-value=6.3 Score=31.35 Aligned_cols=40 Identities=13% Similarity=0.268 Sum_probs=31.9
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHh
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQ 86 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 86 (234)
+.+..-|.+|+.+.. +++. .+=||.||++|+.+||..+-+
T Consensus 40 iK~FdcCsLtLqPc~--dPvi-t~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 40 IKPFDCCSLTLQPCR--DPVI-TPDGYLFDREAILEYILAQKK 79 (303)
T ss_pred cCCcceeeeeccccc--CCcc-CCCCeeeeHHHHHHHHHHHHH
Confidence 455778999999885 5544 488999999999999977644
No 167
>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=64.82 E-value=1 Score=25.13 Aligned_cols=25 Identities=36% Similarity=0.871 Sum_probs=21.2
Q ss_pred CcccCccccccccccCCCCCCCCCC
Q 048114 155 RESVCPDCNRMFCAQCKVPWHAGIR 179 (234)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~H~~~~ 179 (234)
..++|..|+..+|..|....|.++.
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred eEEEecCCCCccCccCCCCCCCCCE
Confidence 4489999999999999887788753
No 168
>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=64.76 E-value=4.6 Score=27.98 Aligned_cols=28 Identities=39% Similarity=0.813 Sum_probs=18.4
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.+.|| .|+..|.--+. .-+.||+||..|
T Consensus 9 KR~Cp--~CG~kFYDLnk---~PivCP~CG~~~ 36 (108)
T PF09538_consen 9 KRTCP--SCGAKFYDLNK---DPIVCPKCGTEF 36 (108)
T ss_pred cccCC--CCcchhccCCC---CCccCCCCCCcc
Confidence 35798 88876553222 227899998875
No 169
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.53 E-value=7.8 Score=22.03 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=7.7
Q ss_pred CcccCCCCCceee
Q 048114 206 NWRRCPNCKIFVE 218 (234)
Q Consensus 206 ~~k~CP~C~~~i~ 218 (234)
..-+||.|+..|.
T Consensus 18 ~~irC~~CG~rIl 30 (44)
T smart00659 18 DVVRCRECGYRIL 30 (44)
T ss_pred CceECCCCCceEE
Confidence 4456776666553
No 170
>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=63.33 E-value=7.2 Score=29.00 Aligned_cols=31 Identities=23% Similarity=0.508 Sum_probs=20.2
Q ss_pred CCeecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 132 AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 132 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+....|| .|..-+...+... ..+.||.||..
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~~-~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAME-LNFTCPRCGAM 137 (158)
T ss_pred CCeEECC--CCCcEeeHHHHHH-cCCcCCCCCCE
Confidence 4456799 7887666554322 34888888765
No 171
>PF14369 zf-RING_3: zinc-finger
Probab=63.03 E-value=9.2 Score=20.52 Aligned_cols=30 Identities=20% Similarity=0.732 Sum_probs=18.8
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
..||- .|...+....... ..+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~~-~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSPD-SDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCCC-CCcCCcCCCCcE
Confidence 35888 8998877643222 224688887654
No 172
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=62.87 E-value=16 Score=25.18 Aligned_cols=54 Identities=19% Similarity=0.605 Sum_probs=33.9
Q ss_pred cccccccccCCCCCCcee-----eCCC---CChhhHHHHHHHHHHHHhc--CCccccCCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFS-----IKGC---SHSYCTECMTKYVASKLQE--NITSINCPVADCKGV 102 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~-----~~~C---~H~fC~~Cl~~~~~~~i~~--~~~~i~CP~~~C~~~ 102 (234)
..+|..|..........- ...| .-.||..||...+.+.+.+ ....-.|| .|...
T Consensus 7 g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crgi 70 (105)
T PF10497_consen 7 GKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRGI 70 (105)
T ss_pred CCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECC--CCCCe
Confidence 456777766443222111 1356 6679999999988877655 23467899 66543
No 173
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.23 E-value=2.7 Score=32.98 Aligned_cols=37 Identities=30% Similarity=0.713 Sum_probs=24.9
Q ss_pred CcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeee
Q 048114 155 RESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEK 219 (234)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k 219 (234)
+.+.+ ||+.|||-|.-.|= ....+.+.||-|+..|..
T Consensus 60 PVvTl--CGHLFCWpClyqWl--------------------------~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 60 PVVTL--CGHLFCWPCLYQWL--------------------------QTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CEEee--cccceehHHHHHHH--------------------------hhcCCCeeCCcccccccc
Confidence 34555 99999999976551 123455788988876654
No 174
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=62.09 E-value=3.1 Score=27.20 Aligned_cols=29 Identities=28% Similarity=0.673 Sum_probs=16.2
Q ss_pred CcccCCCCC----c--eeeeccCCCceEec-CCCCC
Q 048114 206 NWRRCPNCK----I--FVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 206 ~~k~CP~C~----~--~i~k~~GCnhm~C~-C~~~F 234 (234)
..=.||.|+ + -|.|..|=.+++|. ||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 445899999 2 44467788899996 99765
No 175
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=62.06 E-value=1.7 Score=25.30 Aligned_cols=35 Identities=20% Similarity=0.483 Sum_probs=28.9
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYV 81 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 81 (234)
.++|.+|-+.++..+..+..-||.--|..||+.-.
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhH
Confidence 67899999988877766666899999999998633
No 176
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=61.77 E-value=3.9 Score=22.71 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=13.7
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
.|| .|+..+............|+.|+.
T Consensus 1 ~CP--~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCP--RCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred CcC--CCCcccceEEECCEEEEECCCCCe
Confidence 367 777654443333333445655544
No 177
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=61.60 E-value=6.6 Score=20.67 Aligned_cols=23 Identities=26% Similarity=0.635 Sum_probs=13.7
Q ss_pred CCCCceecCCCCccCcccCccccccc
Q 048114 141 DCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 141 ~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
+|+..+..... ..++|+.||..+
T Consensus 5 ~Cg~~~~~~~~---~~irC~~CG~RI 27 (32)
T PF03604_consen 5 ECGAEVELKPG---DPIRCPECGHRI 27 (32)
T ss_dssp SSSSSE-BSTS---STSSBSSSS-SE
T ss_pred cCCCeeEcCCC---CcEECCcCCCeE
Confidence 77776664332 338999998754
No 178
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=61.40 E-value=9 Score=29.78 Aligned_cols=19 Identities=26% Similarity=0.662 Sum_probs=14.9
Q ss_pred CCCeecCCCCCCCCceecC
Q 048114 131 GAQKFYCPFKDCSALLIDD 149 (234)
Q Consensus 131 ~~~~~~Cp~~~C~~~~~~~ 149 (234)
.++++-||+|+|..++..+
T Consensus 135 sSqRIACPRpnCkRiInL~ 153 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLD 153 (275)
T ss_pred ccceeccCCCCcceeeecC
Confidence 3456789999999987765
No 179
>PHA02929 N1R/p28-like protein; Provisional
Probab=61.03 E-value=4.6 Score=32.19 Aligned_cols=39 Identities=23% Similarity=0.589 Sum_probs=22.1
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW 174 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 174 (234)
...|| =|...+..++........=+.|++.||..|...|
T Consensus 174 ~~eC~--ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~W 212 (238)
T PHA02929 174 DKECA--ICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW 212 (238)
T ss_pred CCCCc--cCCcccccCccccccceecCCCCCcccHHHHHHH
Confidence 35688 6776544322111111233479999999997655
No 180
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=59.86 E-value=6.6 Score=23.75 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=18.5
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~ 232 (234)
...+-.||+||.+... |-.|. ||+
T Consensus 24 ~~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC-----eEECCCCCc
Confidence 4566789999998754 88884 885
No 181
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=59.59 E-value=17 Score=25.90 Aligned_cols=37 Identities=16% Similarity=0.450 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCcccCCCCCc---eeeeccCCCceEec-CCCC
Q 048114 195 DIMLMTLAQKENWRRCPNCKI---FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 195 ~~~l~~~~~~~~~k~CP~C~~---~i~k~~GCnhm~C~-C~~~ 233 (234)
+..+..++ ...-.||.|+. .+.|.++=-.|.|. ||+.
T Consensus 83 ~~~L~~fI--~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 83 QDLLDKFI--KEYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHHH--CHHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHHH--HHEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 33444444 44679999998 46677888999996 9974
No 182
>smart00336 BBOX B-Box-type zinc finger.
Probab=59.21 E-value=5.9 Score=21.67 Aligned_cols=24 Identities=29% Similarity=0.790 Sum_probs=19.8
Q ss_pred CcccCccccccccccCCCCCCCCC
Q 048114 155 RESVCPDCNRMFCAQCKVPWHAGI 178 (234)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~H~~~ 178 (234)
..++|..|...+|..|....|.++
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred eEEECCCCCcccccccChhhcCCC
Confidence 348999999999999987677664
No 183
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=58.96 E-value=8.1 Score=32.09 Aligned_cols=48 Identities=19% Similarity=0.591 Sum_probs=32.7
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
.....|+||+.... ++..+..=|=.||..|+.+|+.. .| .||..+++.
T Consensus 298 ~~~~~CpvClk~r~--Nptvl~vSGyVfCY~Ci~~Yv~~---~~----~CPVT~~p~ 345 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQ--NPTVLEVSGYVFCYPCIFSYVVN---YG----HCPVTGYPA 345 (357)
T ss_pred CccccChhHHhccC--CCceEEecceEEeHHHHHHHHHh---cC----CCCccCCcc
Confidence 34567999987654 33333345888999999999972 12 588666653
No 184
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=58.56 E-value=5.3 Score=22.48 Aligned_cols=17 Identities=29% Similarity=0.972 Sum_probs=12.1
Q ss_pred ccCccccccccccCCCC
Q 048114 157 SVCPDCNRMFCAQCKVP 173 (234)
Q Consensus 157 ~~C~~C~~~~C~~C~~~ 173 (234)
+.|+.|+..||...+.+
T Consensus 14 ~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 14 FKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp EE-TTTS-EE-TTTHST
T ss_pred eECCCCCcccCccccCc
Confidence 89999999999988764
No 186
>PHA02862 5L protein; Provisional
Probab=58.36 E-value=15 Score=26.82 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=33.3
Q ss_pred ccccccccCCCCCCceeeCCCCC-----hhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114 48 FICDICVEPKSTDESFSIKGCSH-----SYCTECMTKYVASKLQENITSINCPVADCKGVLEP 105 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 105 (234)
..|=||+++-.. .. -+|.. ....+||.+|+.. ..+..|+ .|+..+..
T Consensus 3 diCWIC~~~~~e--~~--~PC~C~GS~K~VHq~CL~~WIn~-----S~k~~Ce--LCkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDE--RN--NFCGCNEEYKVVHIKCMQLWINY-----SKKKECN--LCKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC--Cc--ccccccCcchhHHHHHHHHHHhc-----CCCcCcc--CCCCeEEE
Confidence 469999987542 22 36644 4899999999942 3567899 88877654
No 187
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=58.16 E-value=16 Score=26.17 Aligned_cols=53 Identities=23% Similarity=0.492 Sum_probs=37.4
Q ss_pred CCcccccccccCCCCCCcee-eCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDESFS-IKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
.+-++|.||.|.-....... -.-||=+.|..|-...|+-.- ..-.|| .|+..+
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCP--vCkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCP--VCKTSF 131 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCC--cccccc
Confidence 35789999998764333222 136899999999999997542 455899 787654
No 188
>PLN02400 cellulose synthase
Probab=57.14 E-value=6.8 Score=37.92 Aligned_cols=60 Identities=20% Similarity=0.470 Sum_probs=40.3
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~ 215 (234)
-|. -|+.-+-...+. ..-+.|..|+...|..|.. |++ +.+.+-||.|+.
T Consensus 38 iCq--ICGD~VG~t~dG-e~FVAC~eCaFPVCRpCYE----------YER------------------keGnq~CPQCkT 86 (1085)
T PLN02400 38 ICQ--ICGDDVGVTETG-DVFVACNECAFPVCRPCYE----------YER------------------KDGTQCCPQCKT 86 (1085)
T ss_pred eee--ecccccCcCCCC-CEEEEEccCCCccccchhh----------eec------------------ccCCccCcccCC
Confidence 455 566544443322 3458999999999996643 222 456689999999
Q ss_pred eeeeccCCCce
Q 048114 216 FVEKKEGCRYM 226 (234)
Q Consensus 216 ~i~k~~GCnhm 226 (234)
...+--|+..+
T Consensus 87 rYkR~KgsprV 97 (1085)
T PLN02400 87 RYRRHKGSPRV 97 (1085)
T ss_pred ccccccCCCCC
Confidence 88877777654
No 189
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.96 E-value=12 Score=30.02 Aligned_cols=56 Identities=18% Similarity=0.534 Sum_probs=38.2
Q ss_pred CCcccccccccCCCCCCce-eeCCCC-----ChhhHHHHHHHHHHHHhc-CCccccCCCCCCCCC
Q 048114 45 ETSFICDICVEPKSTDESF-SIKGCS-----HSYCTECMTKYVASKLQE-NITSINCPVADCKGV 102 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~-~~~~C~-----H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~ 102 (234)
+....|=|||..-+.+... =+-||. |-....|+..|+.++-.. ..-.+.|| .|+..
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~--QCqTE 80 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCP--QCQTE 80 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeech--hhcch
Confidence 4467799999865432211 123674 459999999999876443 35689999 88754
No 190
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=56.90 E-value=8.7 Score=20.96 Aligned_cols=29 Identities=21% Similarity=0.448 Sum_probs=18.1
Q ss_pred ecCCCCCCCCceecCC-CCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDG-GEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~-~~~~~~~~C~~C~~~ 165 (234)
..|+ .|+..+.... ........||.||..
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcC--CCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 4688 8998554332 112455789988863
No 191
>PRK05978 hypothetical protein; Provisional
Probab=56.36 E-value=7.1 Score=28.70 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=16.8
Q ss_pred cccCCCCCc-eeeeccCCCceEec-CCCCC
Q 048114 207 WRRCPNCKI-FVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 207 ~k~CP~C~~-~i~k~~GCnhm~C~-C~~~F 234 (234)
..+||+|+. .+.+.-==-+=+|. ||.+|
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred cCcCCCCCCCcccccccccCCCccccCCcc
Confidence 469999998 44432222344664 77665
No 192
>PLN02436 cellulose synthase A
Probab=56.13 E-value=9.8 Score=36.86 Aligned_cols=60 Identities=20% Similarity=0.484 Sum_probs=39.1
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~ 215 (234)
-|. -|+.-+-...+. ..-+.|..|+...|..|.. |.+ +...+.||.|+.
T Consensus 38 iCq--ICGD~Vg~t~dG-e~FVACn~C~fpvCr~Cye----------yer------------------~eg~~~Cpqckt 86 (1094)
T PLN02436 38 TCQ--ICGDEIELTVDG-EPFVACNECAFPVCRPCYE----------YER------------------REGNQACPQCKT 86 (1094)
T ss_pred ccc--ccccccCcCCCC-CEEEeeccCCCccccchhh----------hhh------------------hcCCccCcccCC
Confidence 455 566554433222 3458999999999986643 222 356688999998
Q ss_pred eeeeccCCCce
Q 048114 216 FVEKKEGCRYM 226 (234)
Q Consensus 216 ~i~k~~GCnhm 226 (234)
...+--|++.+
T Consensus 87 ~Y~r~kgs~~~ 97 (1094)
T PLN02436 87 RYKRIKGSPRV 97 (1094)
T ss_pred chhhccCCCCc
Confidence 87766666544
No 193
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.33 E-value=9.8 Score=37.48 Aligned_cols=18 Identities=28% Similarity=0.781 Sum_probs=14.6
Q ss_pred ccCccccc----cccccCCCCC
Q 048114 157 SVCPDCNR----MFCAQCKVPW 174 (234)
Q Consensus 157 ~~C~~C~~----~~C~~C~~~~ 174 (234)
..||.||. .+|..|+...
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EECCCCCCccccccCcccCCcC
Confidence 78999985 5899998754
No 194
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=55.11 E-value=8.8 Score=30.62 Aligned_cols=58 Identities=16% Similarity=0.283 Sum_probs=36.5
Q ss_pred HHHhccCCHHHHHHHHHHHHHH-HHh--CCCeecCCCCCCCCceecCC----CCccCcccCcccccc
Q 048114 106 EYCRDILPEDVFNRWGNALCEA-VIL--GAQKFYCPFKDCSALLIDDG----GEAIRESVCPDCNRM 165 (234)
Q Consensus 106 ~~i~~~l~~~~~~~~~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~----~~~~~~~~C~~C~~~ 165 (234)
+.+..-++++++..|.+..... -.. .-....|- +|...+.... ......++||.||..
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 3566678999999999887653 110 11123687 8887766442 113455899999864
No 195
>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=55.02 E-value=7.7 Score=26.67 Aligned_cols=26 Identities=27% Similarity=0.786 Sum_probs=16.8
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.|| .|+.-+..... ..+.||.|++.|
T Consensus 4 ~CP--~C~seytY~dg---~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG---TQLICPSCLYEW 29 (109)
T ss_pred cCC--cCCCcceEecC---CeeECccccccc
Confidence 477 78866555433 338888887764
No 196
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.01 E-value=9.4 Score=35.84 Aligned_cols=40 Identities=28% Similarity=0.633 Sum_probs=30.8
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
-.|..|--.+. -++.-..|||+|...|+. + ..-.|| .|..
T Consensus 841 skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e--------~--~~~~CP--~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLD--LPFVHFLCGHSYHQHCLE--------D--KEDKCP--KCLP 880 (933)
T ss_pred eeecccCCccc--cceeeeecccHHHHHhhc--------c--CcccCC--ccch
Confidence 47999977765 455556999999999997 2 345799 8875
No 197
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=54.50 E-value=3.5 Score=37.91 Aligned_cols=30 Identities=27% Similarity=0.847 Sum_probs=21.8
Q ss_pred ccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCcee
Q 048114 160 PDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFV 217 (234)
Q Consensus 160 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i 217 (234)
++|++.||..|.+. ....+.++||+|+...
T Consensus 659 ~kC~H~FC~~Cvq~----------------------------r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 659 TKCGHVFCEECVQT----------------------------RYETRQRKCPKCNAAF 688 (698)
T ss_pred HhcchHHHHHHHHH----------------------------HHHHhcCCCCCCCCCC
Confidence 37899999988652 1134568999999764
No 198
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=54.49 E-value=13 Score=22.20 Aligned_cols=19 Identities=26% Similarity=0.576 Sum_probs=13.7
Q ss_pred HHHHHhcCCcccCCCCCce
Q 048114 198 LMTLAQKENWRRCPNCKIF 216 (234)
Q Consensus 198 l~~~~~~~~~k~CP~C~~~ 216 (234)
+.++.....+..||+|+..
T Consensus 37 ~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 37 LNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHcCCCeEECcCCCcc
Confidence 3444445678999999975
No 199
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=54.42 E-value=7.7 Score=27.76 Aligned_cols=24 Identities=38% Similarity=0.905 Sum_probs=17.5
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
.+|| .|+..++...+. ++||.|++
T Consensus 29 ~hCp--~Cg~PLF~KdG~----v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFRKDGE----VFCPVCGY 52 (131)
T ss_pred hhCc--ccCCcceeeCCe----EECCCCCc
Confidence 3799 899877764332 88888875
No 200
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.86 E-value=14 Score=28.01 Aligned_cols=59 Identities=24% Similarity=0.368 Sum_probs=30.1
Q ss_pred CCHHHHhccCCHHHHHHHHHHHHHHHH--hCCCeecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 103 LEPEYCRDILPEDVFNRWGNALCEAVI--LGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 103 l~~~~i~~~l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
++.+.+...+..+.. +..+.+.+..- .......|| .|+.-+...+.. ...+.||.||..
T Consensus 85 l~~~~i~d~ik~~~~-~~~~klk~~l~~e~~~~~Y~Cp--~C~~rytf~eA~-~~~F~Cp~Cg~~ 145 (178)
T PRK06266 85 PELEKLPEIIKKKKM-EELKKLKEQLEEEENNMFFFCP--NCHIRFTFDEAM-EYGFRCPQCGEM 145 (178)
T ss_pred eCHHHHHHHHHHHHH-HHHHHHHHHhhhccCCCEEECC--CCCcEEeHHHHh-hcCCcCCCCCCC
Confidence 455555555443332 22222322222 234456899 688766655432 234788877764
No 201
>PRK11827 hypothetical protein; Provisional
Probab=53.58 E-value=13 Score=22.80 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=21.0
Q ss_pred cccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 207 WRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 207 ~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
+-.||.|+-..+-..+=+.+.|. |+--|
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeec
Confidence 45899999988766665778895 87543
No 202
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=53.46 E-value=25 Score=21.12 Aligned_cols=46 Identities=24% Similarity=0.578 Sum_probs=30.4
Q ss_pred ccccccccCCCCCCce-eeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 48 FICDICVEPKSTDESF-SIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
-.|..|-.+++.+..- .+-+=..+||.+|....+ .-.|| .|+..|.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l---------~~~CP--NCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETML---------NGVCP--NCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHh---------cCcCc--CCCCccc
Confidence 3589998888765522 221225679999997765 23588 7876654
No 203
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=53.22 E-value=7.5 Score=24.90 Aligned_cols=48 Identities=23% Similarity=0.583 Sum_probs=32.0
Q ss_pred cccccccCCCCC---------Cce-eeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC
Q 048114 49 ICDICVEPKSTD---------ESF-SIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV 102 (234)
Q Consensus 49 ~C~iC~~~~~~~---------~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 102 (234)
+|.||.-+|... +.+ ..--|.|.|-.-|+.+|+....++ -.|| -|.+.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq----~~CP--mcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ----GQCP--MCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc----ccCC--cchhe
Confidence 788888777422 222 122688999999999999766544 3578 56544
No 204
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=53.13 E-value=11 Score=36.43 Aligned_cols=57 Identities=21% Similarity=0.519 Sum_probs=37.0
Q ss_pred CCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeeec
Q 048114 141 DCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKK 220 (234)
Q Consensus 141 ~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~ 220 (234)
-|+.-+-.+.+. ..-+.|..|+...|..|. +|.+ +...+.||.|+....+-
T Consensus 20 iCGd~vg~~~~G-e~FVAC~eC~fpvCr~cy----------eye~------------------~~g~~~cp~c~t~y~~~ 70 (1044)
T PLN02915 20 VCGDEVGVKEDG-QPFVACHVCGFPVCKPCY----------EYER------------------SEGNQCCPQCNTRYKRH 70 (1044)
T ss_pred ccccccCcCCCC-CEEEEeccCCCccccchh----------hhhh------------------hcCCccCCccCCchhhh
Confidence 455544443222 345899999999998664 3322 35668899999887765
Q ss_pred cCCCce
Q 048114 221 EGCRYM 226 (234)
Q Consensus 221 ~GCnhm 226 (234)
-|.+.+
T Consensus 71 ~~~~~~ 76 (1044)
T PLN02915 71 KGCPRV 76 (1044)
T ss_pred cCCCCc
Confidence 566544
No 205
>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=53.12 E-value=5.9 Score=20.52 Aligned_cols=26 Identities=27% Similarity=0.673 Sum_probs=11.4
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.|| .|+.-.... +...+.|+.|+..|
T Consensus 4 ~Cp--~C~se~~y~---D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCP--LCGSEYTYE---DGELLVCPECGHEW 29 (30)
T ss_dssp --T--TT-----EE----SSSEEETTTTEEE
T ss_pred CCC--CCCCcceec---cCCEEeCCcccccC
Confidence 366 676544332 23348888887653
No 206
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=52.56 E-value=11 Score=23.52 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=21.3
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCA 168 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (234)
+.|| +|++....-. .....+.|..||...+.
T Consensus 20 VkCp--dC~N~q~vFs-hast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP--DCGNEQVVFS-HASTVVTCLICGTTLAE 50 (67)
T ss_pred EECC--CCCCEEEEec-cCceEEEecccccEEEe
Confidence 5799 9997544422 23455899999988764
No 207
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=52.33 E-value=41 Score=19.06 Aligned_cols=26 Identities=23% Similarity=0.400 Sum_probs=17.3
Q ss_pred ccCCCCCce-eeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKIF-VEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~-i~k~~GCnhm~C~-C~~~ 233 (234)
-.||.|+.. +-+..+=....|+ |+++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 469999983 3344455567775 8764
No 208
>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=52.31 E-value=8.5 Score=17.24 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=12.3
Q ss_pred ccccCCCCCCCCCChh
Q 048114 166 FCAQCKVPWHAGIRCA 181 (234)
Q Consensus 166 ~C~~C~~~~H~~~~C~ 181 (234)
.|+.|++.-|....|.
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 5888888888776664
No 209
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.70 E-value=13 Score=34.38 Aligned_cols=31 Identities=26% Similarity=0.858 Sum_probs=20.2
Q ss_pred CeecCCCCCCCCceecCCCCccCcccCcccccc------ccccCCCC
Q 048114 133 QKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM------FCAQCKVP 173 (234)
Q Consensus 133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~------~C~~C~~~ 173 (234)
+.++|+ .|+..+.. ..|+.||+. ||..|+..
T Consensus 14 ~akFC~--~CG~~l~~--------~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 14 NNRFCQ--KCGTSLTH--------KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCcccc--ccCCCCCC--------CcCCCCCCCCCcccccccccCCc
Confidence 345777 77765421 368888655 88888764
No 210
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=51.43 E-value=8.2 Score=19.16 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=15.0
Q ss_pred ccCCCCCCCCCCCHHHHhccCC
Q 048114 92 INCPVADCKGVLEPEYCRDILP 113 (234)
Q Consensus 92 i~CP~~~C~~~l~~~~i~~~l~ 113 (234)
+.|| .|...++...+...|+
T Consensus 2 v~CP--iC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCP--VCFREVPENLINSHLD 21 (26)
T ss_pred CcCC--CCcCcccHHHHHHHHH
Confidence 5799 8988887777766655
No 211
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.27 E-value=18 Score=24.02 Aligned_cols=17 Identities=12% Similarity=0.726 Sum_probs=14.5
Q ss_pred hhhHHHHHHHHHHHHhc
Q 048114 71 SYCTECMTKYVASKLQE 87 (234)
Q Consensus 71 ~fC~~Cl~~~~~~~i~~ 87 (234)
-||+.||..|+..+...
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887654
No 212
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.19 E-value=20 Score=27.08 Aligned_cols=59 Identities=19% Similarity=0.436 Sum_probs=37.4
Q ss_pred CCcccccccccCCCCC----CceeeCCCCChhhHHHHHHHHHHHHhcC----CccccCCCCCCCCCCCH
Q 048114 45 ETSFICDICVEPKSTD----ESFSIKGCSHSYCTECMTKYVASKLQEN----ITSINCPVADCKGVLEP 105 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~----~~~i~CP~~~C~~~l~~ 105 (234)
+..-.|.||+...... ..--...||..|..-|+..|+..-+... +..=.|| .|..++..
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pial 229 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIAL 229 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCccee
Confidence 4455688887644211 1112248999999999999998765432 2233788 88776653
No 213
>PRK10220 hypothetical protein; Provisional
Probab=50.84 E-value=11 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.786 Sum_probs=16.5
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.|| .|+.-+..... ..+.||.|+++|
T Consensus 5 ~CP--~C~seytY~d~---~~~vCpeC~hEW 30 (111)
T PRK10220 5 HCP--KCNSEYTYEDN---GMYICPECAHEW 30 (111)
T ss_pred cCC--CCCCcceEcCC---CeEECCcccCcC
Confidence 477 78766555433 337888887764
No 214
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.60 E-value=15 Score=23.19 Aligned_cols=46 Identities=24% Similarity=0.637 Sum_probs=30.1
Q ss_pred cccccccCCCCCCceeeCCC--CChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114 49 ICDICVEPKSTDESFSIKGC--SHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE 106 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 106 (234)
.|..|-.+++++..-.+ -| .|.||.+|.+.-+ .=.|| .|+..|...
T Consensus 7 nCECCDrDLpp~s~dA~-ICtfEcTFCadCae~~l---------~g~CP--nCGGelv~R 54 (84)
T COG3813 7 NCECCDRDLPPDSTDAR-ICTFECTFCADCAENRL---------HGLCP--NCGGELVAR 54 (84)
T ss_pred CCcccCCCCCCCCCcee-EEEEeeehhHhHHHHhh---------cCcCC--CCCchhhcC
Confidence 48888888865443222 34 6889999996554 23588 888765433
No 215
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=50.53 E-value=15 Score=26.95 Aligned_cols=32 Identities=19% Similarity=0.466 Sum_probs=18.9
Q ss_pred CCeecCCCCCCCCceecCCCC----ccCcccCcccccc
Q 048114 132 AQKFYCPFKDCSALLIDDGGE----AIRESVCPDCNRM 165 (234)
Q Consensus 132 ~~~~~Cp~~~C~~~~~~~~~~----~~~~~~C~~C~~~ 165 (234)
.....|| .|+..+...+.. ....+.||.||..
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 3456899 899766653211 1222778877764
No 216
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=49.90 E-value=4.1 Score=33.46 Aligned_cols=75 Identities=20% Similarity=0.403 Sum_probs=41.2
Q ss_pred ccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHH-HHHh-----CCCeecCCCCCCCCceecCC------CCccCcc
Q 048114 90 TSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCE-AVIL-----GAQKFYCPFKDCSALLIDDG------GEAIRES 157 (234)
Q Consensus 90 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~-~~~~-----~~~~~~Cp~~~C~~~~~~~~------~~~~~~~ 157 (234)
.++.|| .|.. .-+++..+...|..+.-- .... .+....|- .|+..+...+ .......
T Consensus 321 LPi~CP--~Csl-------~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY 389 (421)
T COG5151 321 LPISCP--ICSL-------QLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VCQGPFPKPPVSPFDESTSSGRY 389 (421)
T ss_pred CCccCc--chhH-------HHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--eccCCCCCCCCCcccccccccce
Confidence 678888 6642 223344444555444311 1111 12223566 6777555432 1223457
Q ss_pred cCccccccccccCCCCCC
Q 048114 158 VCPDCNRMFCAQCKVPWH 175 (234)
Q Consensus 158 ~C~~C~~~~C~~C~~~~H 175 (234)
+|+.|+..||..|..-.|
T Consensus 390 ~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 390 QCELCKSTFCSDCDVFIH 407 (421)
T ss_pred echhhhhhhhhhhHHHHH
Confidence 999999999998876444
No 217
>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=49.65 E-value=6.6 Score=21.14 Aligned_cols=31 Identities=19% Similarity=0.648 Sum_probs=16.1
Q ss_pred hhHHHHHHHHHHHHhc-CCccccCCCCCCCCCCC
Q 048114 72 YCTECMTKYVASKLQE-NITSINCPVADCKGVLE 104 (234)
Q Consensus 72 fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~l~ 104 (234)
+|.+|+++|....-.. ....+.|+ .|+-.++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~--~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCT--NCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BT--TCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCC--CCCCCEE
Confidence 5889999887543211 34578898 7875554
No 218
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.43 E-value=6.3 Score=32.17 Aligned_cols=31 Identities=26% Similarity=0.726 Sum_probs=23.0
Q ss_pred cccccccccCCCCCCceeeCCCCCh-hhHHHHHHH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHS-YCTECMTKY 80 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 80 (234)
...|.||++--. +.+- ++|||. -|..|-+.+
T Consensus 300 ~~LC~ICmDaP~--DCvf-LeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 300 RRLCAICMDAPR--DCVF-LECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHHhcCCc--ceEE-eecCcEEeehhhcccc
Confidence 567999998643 5554 599999 788886543
No 219
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=49.28 E-value=8.2 Score=18.86 Aligned_cols=8 Identities=50% Similarity=1.007 Sum_probs=6.3
Q ss_pred cccCCCCC
Q 048114 207 WRRCPNCK 214 (234)
Q Consensus 207 ~k~CP~C~ 214 (234)
.-.||+|+
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35899997
No 220
>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=49.19 E-value=12 Score=22.07 Aligned_cols=36 Identities=17% Similarity=0.529 Sum_probs=25.1
Q ss_pred ccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHH
Q 048114 48 FICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVAS 83 (234)
Q Consensus 48 ~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~ 83 (234)
..|.+|...|.... ......||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 35889987775321 2334589999999999876543
No 221
>PLN03086 PRLI-interacting factor K; Provisional
Probab=47.87 E-value=14 Score=33.52 Aligned_cols=30 Identities=20% Similarity=0.511 Sum_probs=25.6
Q ss_pred CCcccCCC--CCceeeeccCCCceEec-CCCCC
Q 048114 205 ENWRRCPN--CKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 205 ~~~k~CP~--C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
.+...||+ |+..+.+...=+|.+|. ||..|
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCcc
Confidence 45678994 99999999999999995 98765
No 222
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.52 E-value=7.4 Score=35.36 Aligned_cols=36 Identities=22% Similarity=0.569 Sum_probs=25.9
Q ss_pred cccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHH
Q 048114 47 SFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVA 82 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~ 82 (234)
...|+||+..|.... ....+.|||..|..|++....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 456999987774322 223459999999999987653
No 223
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.43 E-value=11 Score=31.19 Aligned_cols=32 Identities=28% Similarity=0.596 Sum_probs=21.4
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKY 80 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 80 (234)
-+.|.-|--.+. -.-.+.+|.|.||.+|.+..
T Consensus 90 VHfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIA--IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcce--eeecccccchhhhhhhhhcC
Confidence 457888844332 22235699999999998653
No 224
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.61 E-value=8.2 Score=34.01 Aligned_cols=35 Identities=20% Similarity=0.689 Sum_probs=24.1
Q ss_pred cccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeee
Q 048114 161 DCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEK 219 (234)
Q Consensus 161 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k 219 (234)
.||..||+.|.-. | | .+.....++.||-|+..|-.
T Consensus 203 ~CGHiFC~~CiLq---------y--~-------------~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQ---------Y--W-------------NYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHH---------H--H-------------hhhcccCCccCCchhhhccc
Confidence 4899999988542 1 1 11134678999999988754
No 225
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=45.64 E-value=4.2 Score=37.26 Aligned_cols=59 Identities=29% Similarity=0.574 Sum_probs=41.5
Q ss_pred hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114 43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 110 (234)
++....+|+||+..+. .+ .++.|.|.||..|+..-+...- ....|| -|...+....++.
T Consensus 17 ~~~k~lEc~ic~~~~~--~p-~~~kc~~~~l~~~~n~~f~~~~----~~~~~~--lc~~~~eK~s~~E 75 (684)
T KOG4362|consen 17 AMQKILECPICLEHVK--EP-SLLKCDHIFLKFCLNKLFESKK----GPKQCA--LCKSDIEKRSLRE 75 (684)
T ss_pred HHhhhccCCceeEEee--cc-chhhhhHHHHhhhhhceeeccC----ccccch--hhhhhhhhhhccc
Confidence 3466889999999875 22 4569999999999987775331 256777 6776555555444
No 226
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=45.63 E-value=21 Score=21.28 Aligned_cols=31 Identities=23% Similarity=0.494 Sum_probs=17.0
Q ss_pred CeecCCCCCCCCc----eecCCCCccCcccCcccccc
Q 048114 133 QKFYCPFKDCSAL----LIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 133 ~~~~Cp~~~C~~~----~~~~~~~~~~~~~C~~C~~~ 165 (234)
..+.|| -|++- +..+......-++||+|.+.
T Consensus 3 ~Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 3 EWILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred eEEECC--CCCCccceeeecCceeccccccCCCCCce
Confidence 346788 78853 22222222334788877664
No 227
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=45.37 E-value=19 Score=29.33 Aligned_cols=26 Identities=23% Similarity=0.460 Sum_probs=20.5
Q ss_pred cccCCCCCceeee--ccCCCceEec-CCC
Q 048114 207 WRRCPNCKIFVEK--KEGCRYMRCS-SNP 232 (234)
Q Consensus 207 ~k~CP~C~~~i~k--~~GCnhm~C~-C~~ 232 (234)
-++||.|+..|+| .+|=.-..|. |+.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 4799999999987 5677778884 764
No 228
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.27 E-value=28 Score=25.12 Aligned_cols=14 Identities=14% Similarity=0.330 Sum_probs=10.3
Q ss_pred eecCCCCCCCCceecC
Q 048114 134 KFYCPFKDCSALLIDD 149 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~ 149 (234)
..+|+ +|+..+...
T Consensus 70 ~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCR--NCGNEWSLK 83 (135)
T ss_pred EEECC--CCCCEEecc
Confidence 45899 999776654
No 229
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=45.24 E-value=18 Score=27.74 Aligned_cols=25 Identities=20% Similarity=0.495 Sum_probs=20.1
Q ss_pred ccCCCCCceeeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
-.|+.|+.++.+.+. |.|.|. ||+.
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCE
Confidence 479999998887444 999995 9863
No 230
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=45.03 E-value=29 Score=22.48 Aligned_cols=18 Identities=17% Similarity=0.763 Sum_probs=16.2
Q ss_pred CCCCChhhHHHHHHHHHH
Q 048114 66 KGCSHSYCTECMTKYVAS 83 (234)
Q Consensus 66 ~~C~H~fC~~Cl~~~~~~ 83 (234)
-.|.|.|..-|+.+|+..
T Consensus 52 G~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred EecchHHHHHHHHHHHhh
Confidence 379999999999999975
No 231
>PLN02195 cellulose synthase A
Probab=45.02 E-value=17 Score=34.99 Aligned_cols=30 Identities=20% Similarity=0.486 Sum_probs=20.7
Q ss_pred CCCCceecCCCCccCcccCccccccccccCC
Q 048114 141 DCSALLIDDGGEAIRESVCPDCNRMFCAQCK 171 (234)
Q Consensus 141 ~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 171 (234)
-|+..+-.+... ..-+.|..|+...|..|.
T Consensus 11 ~cgd~~~~~~~g-~~fvaC~eC~~pvCrpCy 40 (977)
T PLN02195 11 TCGEEVGVDSNG-EAFVACHECSYPLCKACL 40 (977)
T ss_pred ecccccCcCCCC-CeEEEeccCCCccccchh
Confidence 566655544333 345899999999998664
No 232
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.89 E-value=23 Score=28.90 Aligned_cols=28 Identities=29% Similarity=0.548 Sum_probs=22.3
Q ss_pred CcccCCCCCceeee--ccCCCceEec-CCCC
Q 048114 206 NWRRCPNCKIFVEK--KEGCRYMRCS-SNPQ 233 (234)
Q Consensus 206 ~~k~CP~C~~~i~k--~~GCnhm~C~-C~~~ 233 (234)
.-++||.|+..|+| .+|=.--.|. |+..
T Consensus 234 ~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 34799999999986 5788888884 8764
No 233
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.81 E-value=18 Score=22.30 Aligned_cols=21 Identities=29% Similarity=0.732 Sum_probs=16.0
Q ss_pred HHHHhcCCcccCCCCCceeee
Q 048114 199 MTLAQKENWRRCPNCKIFVEK 219 (234)
Q Consensus 199 ~~~~~~~~~k~CP~C~~~i~k 219 (234)
..+..+..+.+||+|...|.-
T Consensus 36 edL~~ge~Va~CpsCSL~I~V 56 (67)
T KOG2923|consen 36 EDLENGEDVARCPSCSLIIRV 56 (67)
T ss_pred HHHhCCCeeecCCCceEEEEE
Confidence 345567888999999988753
No 234
>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=44.54 E-value=17 Score=25.92 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=18.4
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.+.|| .|+..|.--+. .-+.||+||..+
T Consensus 9 Kr~Cp--~cg~kFYDLnk---~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICP--NTGSKFYDLNR---RPAVSPYTGEQF 36 (129)
T ss_pred cccCC--CcCccccccCC---CCccCCCcCCcc
Confidence 35799 88876553222 338899988874
No 235
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=43.95 E-value=12 Score=22.65 Aligned_cols=37 Identities=22% Similarity=0.562 Sum_probs=27.3
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccccccccCCCCC
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW 174 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 174 (234)
.|| -|.........+..+.-.|..|+...|..|+-..
T Consensus 4 ~CP--lCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 4 LCP--LCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred cCC--cccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 477 7776655444455566799999999999998643
No 236
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=43.76 E-value=33 Score=27.58 Aligned_cols=48 Identities=25% Similarity=0.481 Sum_probs=36.5
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG 101 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 101 (234)
.+.|||=+-++. +++.-..|||.|=++=+..++. +...+.||..+|..
T Consensus 176 s~rdPis~~~I~--nPviSkkC~HvydrDsI~~~l~-----~~~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIV--NPVISKKCGHVYDRDSIMQILC-----DEITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhh--chhhhcCcCcchhhhhHHHHhc-----cCceeecccccCCc
Confidence 457888766654 5555569999999988877774 45679999999983
No 237
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.58 E-value=16 Score=28.55 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=20.5
Q ss_pred ccccccCCCCCCceeeCCCCCh-hhHHHH
Q 048114 50 CDICVEPKSTDESFSIKGCSHS-YCTECM 77 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl 77 (234)
|-.|.+.- ..+.++||.|. +|..|=
T Consensus 161 Cr~C~~~~---~~VlllPCrHl~lC~~C~ 186 (207)
T KOG1100|consen 161 CRKCGERE---ATVLLLPCRHLCLCGICD 186 (207)
T ss_pred ceecCcCC---ceEEeecccceEeccccc
Confidence 99998753 45778899998 999996
No 238
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=43.50 E-value=29 Score=18.07 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=19.7
Q ss_pred cCCCCCceeeeccCCCceEec-CCC
Q 048114 209 RCPNCKIFVEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 209 ~CP~C~~~i~k~~GCnhm~C~-C~~ 232 (234)
.|..|+..+.-..|=..+.|. |.+
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 588999998888888888885 753
No 239
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=43.42 E-value=33 Score=32.27 Aligned_cols=50 Identities=22% Similarity=0.472 Sum_probs=33.6
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP 105 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 105 (234)
...|++|+..+.......-.+|+|.||..|+..|-... -.|| .|...++.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a-------qTCP--iDR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA-------QTCP--VDRGEFGE 172 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc-------ccCc--hhhhhhhe
Confidence 34677887666433333345999999999999988633 3678 66655544
No 240
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.06 E-value=24 Score=28.84 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=22.6
Q ss_pred CcccCCCCCceeee--ccCCCceEec-CCC
Q 048114 206 NWRRCPNCKIFVEK--KEGCRYMRCS-SNP 232 (234)
Q Consensus 206 ~~k~CP~C~~~i~k--~~GCnhm~C~-C~~ 232 (234)
.-++|+.|+..|+| -+|=+-..|. |+.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 44799999999997 5899999995 863
No 241
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=42.75 E-value=67 Score=21.42 Aligned_cols=59 Identities=19% Similarity=0.352 Sum_probs=28.6
Q ss_pred CCCHHHHhccCCHH----HHHHHHHHHHHHHHhCCCe-----ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 102 VLEPEYCRDILPED----VFNRWGNALCEAVILGAQK-----FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 102 ~l~~~~i~~~l~~~----~~~~~~~~~~~~~~~~~~~-----~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.++...|..+++.+ .++.+...... ....... -.|- +|++.+..+.-. .-.+||.|+..
T Consensus 18 plt~~ei~~~~~~~~~~~v~~~L~hiak~-lkr~g~~Llv~Pa~Ck--kCGfef~~~~ik--~pSRCP~CKSE 85 (97)
T COG3357 18 PLTVAEIFELLNGEKEKEVYDHLEHIAKS-LKRKGKRLLVRPARCK--KCGFEFRDDKIK--KPSRCPKCKSE 85 (97)
T ss_pred cchHHHHHHHHcCCchHHHHHHHHHHHHH-HHhCCceEEecChhhc--ccCccccccccC--CcccCCcchhh
Confidence 46667777666533 44433333221 1122221 1566 888777653221 12677766543
No 242
>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 PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=42.18 E-value=14 Score=29.45 Aligned_cols=15 Identities=20% Similarity=0.450 Sum_probs=8.6
Q ss_pred CCcccCCCCCceeee
Q 048114 205 ENWRRCPNCKIFVEK 219 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k 219 (234)
.....||.|+.+..+
T Consensus 33 i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 33 IEVTICPKCGRYRIG 47 (236)
T ss_pred cCceECCCCCCEECC
Confidence 345666666665443
No 244
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=42.07 E-value=17 Score=21.97 Aligned_cols=14 Identities=36% Similarity=0.857 Sum_probs=11.0
Q ss_pred CcccCCCCCceeee
Q 048114 206 NWRRCPNCKIFVEK 219 (234)
Q Consensus 206 ~~k~CP~C~~~i~k 219 (234)
.++.||+|+.+.-|
T Consensus 4 ~~rkC~~cg~YTLk 17 (59)
T COG2260 4 LIRKCPKCGRYTLK 17 (59)
T ss_pred hhhcCcCCCceeec
Confidence 45789999988766
No 245
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=42.07 E-value=11 Score=22.92 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=11.2
Q ss_pred ccCCCCCceeeec
Q 048114 208 RRCPNCKIFVEKK 220 (234)
Q Consensus 208 k~CP~C~~~i~k~ 220 (234)
|.||.||.+|.-+
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 7899999999864
No 246
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=41.86 E-value=21 Score=21.76 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=20.4
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCA 168 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (234)
+.|| +|.+....-. .....+.|..|+...+.
T Consensus 12 VkCp--~C~n~q~vFs-ha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCP--DCGNEQVVFS-HASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECC--CCCCeEEEEe-cCCcEEECcccCCCccc
Confidence 5799 9997544322 22345899998887653
No 247
>PF14353 CpXC: CpXC protein
Probab=41.46 E-value=13 Score=26.33 Aligned_cols=45 Identities=27% Similarity=0.546 Sum_probs=25.6
Q ss_pred ccCCCCCCCCCCCHHHHhcc---CCHHHHHHHHHHHHHHHHhC-CCeecCCCCCCCCceec
Q 048114 92 INCPVADCKGVLEPEYCRDI---LPEDVFNRWGNALCEAVILG-AQKFYCPFKDCSALLID 148 (234)
Q Consensus 92 i~CP~~~C~~~l~~~~i~~~---l~~~~~~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~ 148 (234)
|+|| .|+..+..+....+ .++++.++ ++.. -....|| .|+..+..
T Consensus 2 itCP--~C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP--~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCP--HCGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCP--SCGHKFRL 50 (128)
T ss_pred cCCC--CCCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECC--CCCCceec
Confidence 7899 89988776655433 23333332 2221 2335788 88875543
No 248
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=41.39 E-value=21 Score=24.34 Aligned_cols=23 Identities=22% Similarity=0.856 Sum_probs=19.1
Q ss_pred CCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114 66 KGCSHSYCTECMTKYVASKLQENITSINCP 95 (234)
Q Consensus 66 ~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 95 (234)
-.|.|.|..-|+.+|++.. -.||
T Consensus 79 G~CNHaFH~hCisrWlktr-------~vCP 101 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR-------NVCP 101 (114)
T ss_pred eecchHHHHHHHHHHHhhc-------CcCC
Confidence 3799999999999999743 3688
No 249
>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=41.37 E-value=57 Score=22.82 Aligned_cols=36 Identities=28% Similarity=0.488 Sum_probs=23.3
Q ss_pred CeecCCCCCCCCceecCCCCccCcccCccccccccccCCCC
Q 048114 133 QKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVP 173 (234)
Q Consensus 133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 173 (234)
+...|. -|...+..-. .....|..|+..+|..|...
T Consensus 53 ~~~~C~--~C~~~fg~l~---~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCA--RCGKPFGFLF---NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-T--TTS-BCSCTS---TTCEEETTTTEEEETTSEEE
T ss_pred CCcchh--hhCCcccccC---CCCCcCCcCCccccCccCCc
Confidence 345788 7875432211 12289999999999999874
No 250
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.08 E-value=18 Score=24.20 Aligned_cols=40 Identities=18% Similarity=0.331 Sum_probs=32.2
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHh
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQ 86 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 86 (234)
..+.|.||-.++...+.|++.+ .-+...+|+..-...++.
T Consensus 5 kewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 5 KEWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRKKPG 44 (103)
T ss_pred ceeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhcCcC
Confidence 4788999999998888888877 778999999876655543
No 251
>PRK10445 endonuclease VIII; Provisional
Probab=40.82 E-value=24 Score=28.61 Aligned_cols=25 Identities=20% Similarity=0.472 Sum_probs=20.3
Q ss_pred cccCCCCCceeee--ccCCCceEec-CC
Q 048114 207 WRRCPNCKIFVEK--KEGCRYMRCS-SN 231 (234)
Q Consensus 207 ~k~CP~C~~~i~k--~~GCnhm~C~-C~ 231 (234)
-++||.|+..|++ .+|=.-..|. |+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 4799999999996 5787778884 75
No 252
>PLN00209 ribosomal protein S27; Provisional
Probab=40.62 E-value=19 Score=23.72 Aligned_cols=31 Identities=19% Similarity=0.526 Sum_probs=21.4
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCA 168 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (234)
+.|| +|......-. .....+.|..|+..+|.
T Consensus 37 VkCp--~C~n~q~VFS-hA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFS-HSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEe-cCceEEEccccCCEeec
Confidence 5899 9997544322 23455899999988774
No 253
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=40.40 E-value=19 Score=19.80 Aligned_cols=20 Identities=30% Similarity=1.095 Sum_probs=14.0
Q ss_pred ccCCCCCc-eeeec--cCCCceEe
Q 048114 208 RRCPNCKI-FVEKK--EGCRYMRC 228 (234)
Q Consensus 208 k~CP~C~~-~i~k~--~GCnhm~C 228 (234)
+.||.|+. +|+|. .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 58999998 44453 35 66777
No 254
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=40.31 E-value=19 Score=23.64 Aligned_cols=31 Identities=26% Similarity=0.631 Sum_probs=21.6
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCA 168 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (234)
+.|| +|......-. .....+.|..|+..+|.
T Consensus 36 VkCp--~C~n~q~VFS-hA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFS-HAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEe-cCceEEEccccCCEeec
Confidence 5899 9997544322 23455899999988874
No 255
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=40.14 E-value=18 Score=21.85 Aligned_cols=20 Identities=40% Similarity=0.778 Sum_probs=15.2
Q ss_pred HHHHHhcCCcccCCCCCcee
Q 048114 198 LMTLAQKENWRRCPNCKIFV 217 (234)
Q Consensus 198 l~~~~~~~~~k~CP~C~~~i 217 (234)
+..+..+....+||+|...|
T Consensus 35 LeDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 35 LEDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred HHHhhCCceEEEcCCceEEE
Confidence 44556677789999998765
No 256
>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=40.06 E-value=18 Score=24.58 Aligned_cols=24 Identities=33% Similarity=0.977 Sum_probs=17.2
Q ss_pred cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+|| .|+..+.... ..+.|+.|++.
T Consensus 2 fC~--~Cg~~l~~~~----~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCP--KCGSLMTPKN----GVYVCPSCGYE 25 (104)
T ss_pred CCc--ccCcccccCC----CeEECcCCCCc
Confidence 688 8999886532 24788888765
No 257
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.85 E-value=36 Score=31.98 Aligned_cols=34 Identities=24% Similarity=0.598 Sum_probs=18.6
Q ss_pred cCCCCCCCCceecCCCCccCcccCcccccc-----ccccCCCC
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM-----FCAQCKVP 173 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 173 (234)
.|| +|...+..... .+...|..||+. .|..|+..
T Consensus 446 ~Cp--~Cd~~lt~H~~--~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECP--NCDSPLTLHKA--TGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCC--CCCcceEEecC--CCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 355 56655544332 244677777655 56666554
No 258
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=39.75 E-value=3.8 Score=21.13 Aligned_cols=20 Identities=25% Similarity=0.584 Sum_probs=10.4
Q ss_pred cccCCCCCCCCCCCHHHHhc
Q 048114 91 SINCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 91 ~i~CP~~~C~~~l~~~~i~~ 110 (234)
.++||...|...+.......
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~ 21 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSH 21 (30)
T ss_dssp EEE--STT---EEEHHHHHH
T ss_pred ccccccccCcchhhhhhhcc
Confidence 47899999998877655443
No 259
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=39.44 E-value=12 Score=24.95 Aligned_cols=30 Identities=17% Similarity=0.366 Sum_probs=23.1
Q ss_pred CCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 205 ENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
..-..||.|+..-.|..+----.|+ |++.|
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 3446899999988888777778885 88754
No 260
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=39.32 E-value=44 Score=16.49 Aligned_cols=23 Identities=22% Similarity=0.696 Sum_probs=17.8
Q ss_pred CCCCCceeeeccCCCceEec-CCC
Q 048114 210 CPNCKIFVEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 210 CP~C~~~i~k~~GCnhm~C~-C~~ 232 (234)
|-+|+..+.-..|=.++.|. |.+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 55788888888888888885 754
No 261
>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=38.86 E-value=26 Score=28.58 Aligned_cols=25 Identities=24% Similarity=0.394 Sum_probs=19.5
Q ss_pred cccCCCCCceeee--ccCCCceEec-CC
Q 048114 207 WRRCPNCKIFVEK--KEGCRYMRCS-SN 231 (234)
Q Consensus 207 ~k~CP~C~~~i~k--~~GCnhm~C~-C~ 231 (234)
-++||.|+..|+| .+|=.-..|. |+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 4799999999997 4677777773 64
No 262
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.84 E-value=30 Score=28.19 Aligned_cols=26 Identities=23% Similarity=0.458 Sum_probs=20.4
Q ss_pred CcccCCCCCceeee--ccCCCceEec-CC
Q 048114 206 NWRRCPNCKIFVEK--KEGCRYMRCS-SN 231 (234)
Q Consensus 206 ~~k~CP~C~~~i~k--~~GCnhm~C~-C~ 231 (234)
.-++||+|+..|++ .+|=.--.|. |+
T Consensus 243 ~g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 34799999999996 5677777773 75
No 263
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=38.56 E-value=16 Score=22.06 Aligned_cols=16 Identities=31% Similarity=0.424 Sum_probs=8.9
Q ss_pred cccCCCCCceeeeccC
Q 048114 207 WRRCPNCKIFVEKKEG 222 (234)
Q Consensus 207 ~k~CP~C~~~i~k~~G 222 (234)
..+||.|+..++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 4689999999886443
No 264
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=38.36 E-value=48 Score=23.04 Aligned_cols=29 Identities=17% Similarity=0.575 Sum_probs=22.0
Q ss_pred CCcccCCCCCc---eeeeccCCCceEec-CCCC
Q 048114 205 ENWRRCPNCKI---FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~---~i~k~~GCnhm~C~-C~~~ 233 (234)
...-.||.|+. .++|.++=-.|.|. ||++
T Consensus 78 ~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 78 KEYVLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred HhcEECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 34679999998 46677666678896 9974
No 265
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=38.12 E-value=49 Score=23.87 Aligned_cols=29 Identities=14% Similarity=0.477 Sum_probs=21.5
Q ss_pred CCcccCCCCCc---eeeeccCCCceEec-CCCC
Q 048114 205 ENWRRCPNCKI---FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~---~i~k~~GCnhm~C~-C~~~ 233 (234)
...-.||.|+. .+.|.+.=..+.|. ||++
T Consensus 95 ~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 95 RKYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred hheEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 35679999998 45566555567996 9985
No 266
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=37.97 E-value=12 Score=21.49 Aligned_cols=34 Identities=18% Similarity=0.517 Sum_probs=25.9
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA 82 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 82 (234)
.|.||........++.-..|+..|...|+.-...
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 3888888666667777778888888888876554
No 267
>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=37.60 E-value=11 Score=35.54 Aligned_cols=16 Identities=31% Similarity=1.194 Sum_probs=0.0
Q ss_pred ccCcccccc-----ccccCCC
Q 048114 157 SVCPDCNRM-----FCAQCKV 172 (234)
Q Consensus 157 ~~C~~C~~~-----~C~~C~~ 172 (234)
..|+.||.. +|..|+.
T Consensus 668 ~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 668 NRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp ---------------------
T ss_pred hcCcccCCccccceecccccc
Confidence 456666544 4555544
No 268
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=37.17 E-value=19 Score=19.13 Aligned_cols=13 Identities=38% Similarity=0.835 Sum_probs=9.6
Q ss_pred cccCCCCCceeee
Q 048114 207 WRRCPNCKIFVEK 219 (234)
Q Consensus 207 ~k~CP~C~~~i~k 219 (234)
+-.||+|+..|.-
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 4689999998864
No 269
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=37.13 E-value=35 Score=18.42 Aligned_cols=28 Identities=25% Similarity=0.595 Sum_probs=15.1
Q ss_pred cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.|| .|+..+-...........|..||..
T Consensus 3 ~C~--~Cg~~Yh~~~~pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 3 ICP--KCGRIYHIEFNPPKVEGVCDNCGGE 30 (36)
T ss_dssp EET--TTTEEEETTTB--SSTTBCTTTTEB
T ss_pred CcC--CCCCccccccCCCCCCCccCCCCCe
Confidence 466 7776665543333334677777653
No 270
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=36.99 E-value=28 Score=20.89 Aligned_cols=31 Identities=19% Similarity=0.416 Sum_probs=17.8
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCA 168 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (234)
+.|| +|.+....-. .....+.|..|+..+|.
T Consensus 8 VkCp--~C~~~q~vFS-ha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFS-HAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEET-T-SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEe-cCCeEEEcccCCCEecC
Confidence 5799 9997544322 23455899999988875
No 271
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=36.63 E-value=28 Score=32.50 Aligned_cols=39 Identities=26% Similarity=0.510 Sum_probs=31.3
Q ss_pred cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHH
Q 048114 44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVAS 83 (234)
Q Consensus 44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 83 (234)
....+.|.||---+.....+.. .|+|....+|+..|+..
T Consensus 1025 ~~~~~~C~~C~l~V~gss~~Cg-~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSNFCG-TCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ccceeeeeeEeeEeeccchhhc-cccccccHHHHHHHHhc
Confidence 4567789999877766666655 89999999999999973
No 272
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=36.60 E-value=33 Score=23.41 Aligned_cols=40 Identities=23% Similarity=0.433 Sum_probs=31.7
Q ss_pred cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhc
Q 048114 47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQE 87 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 87 (234)
.+.|.||.+++-.++.|++.+ +-....+||+.-....+..
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~-kG~VH~~C~~~~~~~k~~~ 41 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTK-KGPVHYECFREKASKKLYG 41 (101)
T ss_pred ceEEEecCCeeeecceEEEec-CCcEeHHHHHHHHhhhccc
Confidence 578999999998888888744 4778999999877655443
No 273
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.57 E-value=28 Score=26.60 Aligned_cols=23 Identities=22% Similarity=0.624 Sum_probs=19.4
Q ss_pred ccCCCCCceeeeccCCCceEec-CCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~ 232 (234)
..|++|+..+++ .=+.|+|. ||+
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 699999999999 44789994 986
No 274
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=36.55 E-value=34 Score=17.88 Aligned_cols=23 Identities=30% Similarity=0.758 Sum_probs=14.5
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
.|+ .|++++.... ....||.|+.
T Consensus 3 ~C~--~CGy~y~~~~----~~~~CP~Cg~ 25 (33)
T cd00350 3 VCP--VCGYIYDGEE----APWVCPVCGA 25 (33)
T ss_pred ECC--CCCCEECCCc----CCCcCcCCCC
Confidence 366 7887765432 2368888875
No 275
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.53 E-value=30 Score=28.40 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=20.3
Q ss_pred cccCCCCCceeee--ccCCCceEec-CC
Q 048114 207 WRRCPNCKIFVEK--KEGCRYMRCS-SN 231 (234)
Q Consensus 207 ~k~CP~C~~~i~k--~~GCnhm~C~-C~ 231 (234)
-++||.|+..|.| .+|=.-..|. |+
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 5788888884 75
No 276
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=35.82 E-value=54 Score=23.82 Aligned_cols=29 Identities=17% Similarity=0.515 Sum_probs=21.9
Q ss_pred CCcccCCCCCc---eeeeccCCCceEec-CCCC
Q 048114 205 ENWRRCPNCKI---FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~---~i~k~~GCnhm~C~-C~~~ 233 (234)
...-.||.|+. .++|.+.=-.+.|. ||++
T Consensus 100 ~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 100 KEYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred HhcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 34679999998 46676665578996 9985
No 277
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=35.72 E-value=22 Score=24.64 Aligned_cols=11 Identities=36% Similarity=0.845 Sum_probs=6.3
Q ss_pred ccccCCCCCCC
Q 048114 166 FCAQCKVPWHA 176 (234)
Q Consensus 166 ~C~~C~~~~H~ 176 (234)
.|..|+.+-+-
T Consensus 87 ~CM~C~~pLTL 97 (114)
T PF11023_consen 87 ACMHCKEPLTL 97 (114)
T ss_pred ccCcCCCcCcc
Confidence 36667665443
No 278
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=35.47 E-value=19 Score=24.78 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=19.0
Q ss_pred CeecCCCCCCCCceecCCCC--ccCcccCcccccc
Q 048114 133 QKFYCPFKDCSALLIDDGGE--AIRESVCPDCNRM 165 (234)
Q Consensus 133 ~~~~Cp~~~C~~~~~~~~~~--~~~~~~C~~C~~~ 165 (234)
..++|+ .|.+.+...+++ ..-...|.+|.+.
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~v 35 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYV 35 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcce
Confidence 346788 899877766542 3334567666544
No 279
>PRK12495 hypothetical protein; Provisional
Probab=35.37 E-value=61 Score=25.49 Aligned_cols=25 Identities=24% Similarity=0.817 Sum_probs=16.2
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.+|+ .|+..|+...+ ..+|+.|+..
T Consensus 43 ~hC~--~CG~PIpa~pG----~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCD--ECGDPIFRHDG----QEFCPTCQQP 67 (226)
T ss_pred hhcc--cccCcccCCCC----eeECCCCCCc
Confidence 6899 89988874322 1566666543
No 280
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=35.10 E-value=21 Score=20.47 Aligned_cols=35 Identities=26% Similarity=0.587 Sum_probs=25.2
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhc
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQE 87 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 87 (234)
.|.||-.... +.+.+ -+..+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~--~GI~I--~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKE--EGIHI--YGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCC--CCEEE--ECeEehHHHHHHhccCCCCC
Confidence 3889987664 33433 48889999999998766543
No 281
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.09 E-value=28 Score=28.16 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=22.3
Q ss_pred CCcccCCCCCceeeeccCCCceEec-CCCC
Q 048114 205 ENWRRCPNCKIFVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~ 233 (234)
...+.||.||..+....|=..+.|. ||..
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCE
Confidence 4578999999988765555778995 8853
No 282
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=34.80 E-value=17 Score=27.59 Aligned_cols=24 Identities=21% Similarity=0.415 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCcccCCCCCceeee
Q 048114 196 IMLMTLAQKENWRRCPNCKIFVEK 219 (234)
Q Consensus 196 ~~l~~~~~~~~~k~CP~C~~~i~k 219 (234)
..+..+......++|++||.....
T Consensus 146 ~~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 146 PVFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred HHHHHHhcCHhhccCCcCCcccCc
Confidence 345566667788999999997654
No 283
>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=34.68 E-value=30 Score=20.72 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=16.9
Q ss_pred CCcccCCCCCceeeeccCCCceEec-CCC
Q 048114 205 ENWRRCPNCKIFVEKKEGCRYMRCS-SNP 232 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~~GCnhm~C~-C~~ 232 (234)
..+..||+||.+.. .|-.|. ||+
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccCe
Confidence 45678999998653 578884 875
No 284
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=34.51 E-value=36 Score=23.79 Aligned_cols=25 Identities=28% Similarity=0.620 Sum_probs=16.5
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+|+ +|+..+..... ...||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~~----~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECE--DCSEEVSPEID----LYRCPKCHG 94 (115)
T ss_pred EEEcc--cCCCEEecCCc----CccCcCCcC
Confidence 35899 89877655332 266887765
No 285
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.37 E-value=21 Score=22.00 Aligned_cols=16 Identities=25% Similarity=0.256 Sum_probs=12.9
Q ss_pred CCcccCCCCCceeeec
Q 048114 205 ENWRRCPNCKIFVEKK 220 (234)
Q Consensus 205 ~~~k~CP~C~~~i~k~ 220 (234)
....+||.|+..++..
T Consensus 5 ~~~v~CP~Cgkpv~w~ 20 (65)
T COG3024 5 RITVPCPTCGKPVVWG 20 (65)
T ss_pred cccccCCCCCCccccc
Confidence 4568999999998863
No 286
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=34.16 E-value=54 Score=25.46 Aligned_cols=29 Identities=17% Similarity=0.589 Sum_probs=22.5
Q ss_pred CCcccCCCCCc---eeeeccCCCceEec-CCCC
Q 048114 205 ENWRRCPNCKI---FVEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 205 ~~~k~CP~C~~---~i~k~~GCnhm~C~-C~~~ 233 (234)
...-.||.|+. .+.|.++=-.+.|. ||++
T Consensus 96 ~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 96 DEYVICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred HheEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 45679999998 46677776678996 9985
No 287
>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=34.15 E-value=9.4 Score=22.06 Aligned_cols=43 Identities=28% Similarity=0.674 Sum_probs=20.3
Q ss_pred ccccccccCCCCCCceeeCCC-CChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 48 FICDICVEPKSTDESFSIKGC-SHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
+.|--|.-... . +..| .|..|..|+..++.. .-.|| .|+.+|+
T Consensus 3 ~nCKsCWf~~k--~---Li~C~dHYLCl~CLt~ml~~-------s~~C~--iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCWFANK--G---LIKCSDHYLCLNCLTLMLSR-------SDRCP--ICGKPLP 46 (50)
T ss_dssp ----SS-S--S--S---EEE-SS-EEEHHHHHHT-SS-------SSEET--TTTEE--
T ss_pred ccChhhhhcCC--C---eeeecchhHHHHHHHHHhcc-------ccCCC--cccCcCc
Confidence 34666654321 2 2255 799999999877741 23578 7877665
No 288
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=33.91 E-value=18 Score=30.16 Aligned_cols=30 Identities=17% Similarity=0.592 Sum_probs=23.3
Q ss_pred ccccccccCCCCCCceeeCCCCChhhHHHH
Q 048114 48 FICDICVEPKSTDESFSIKGCSHSYCTECM 77 (234)
Q Consensus 48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl 77 (234)
..|-.|+++......+....|.+.||.+|=
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCD 360 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCD 360 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccch
Confidence 348888777766666777789999999995
No 289
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=33.84 E-value=22 Score=17.35 Aligned_cols=18 Identities=22% Similarity=0.626 Sum_probs=14.0
Q ss_pred ccCCCCCCCCCCCHHHHhcc
Q 048114 92 INCPVADCKGVLEPEYCRDI 111 (234)
Q Consensus 92 i~CP~~~C~~~l~~~~i~~~ 111 (234)
+.|| .|+..+..+.+...
T Consensus 3 ~~C~--~CgR~F~~~~l~~H 20 (25)
T PF13913_consen 3 VPCP--ICGRKFNPDRLEKH 20 (25)
T ss_pred CcCC--CCCCEECHHHHHHH
Confidence 5788 89999888777543
No 290
>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=33.74 E-value=32 Score=30.81 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=17.9
Q ss_pred ccCCCCCceeeeccCCCceEe-cCCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRC-SSNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C-~C~~~ 233 (234)
-.||+|.....-...=|.+.| .||++
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCc
Confidence 478888886664334458888 48875
No 291
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.56 E-value=52 Score=18.94 Aligned_cols=32 Identities=22% Similarity=0.542 Sum_probs=21.7
Q ss_pred cccccccCCCCCCceeeCCCCCh-hhHHHHHHH
Q 048114 49 ICDICVEPKSTDESFSIKGCSHS-YCTECMTKY 80 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 80 (234)
.|..|..+......+.-+.|... .|.+|+..-
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 58888877654444555677554 899998744
No 292
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=33.55 E-value=19 Score=26.86 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=14.5
Q ss_pred HHHHHHhcCCcccCCCCCc
Q 048114 197 MLMTLAQKENWRRCPNCKI 215 (234)
Q Consensus 197 ~l~~~~~~~~~k~CP~C~~ 215 (234)
.+..+......++|++||.
T Consensus 141 ~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 141 VFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred HHHHHhCChhhccCCccCC
Confidence 4556666777899999984
No 293
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.51 E-value=37 Score=23.62 Aligned_cols=25 Identities=28% Similarity=0.781 Sum_probs=16.0
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+|+ +|+..+.... ....||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~----~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCW--DCSQVVEIHQ----HDAQCPHCHG 94 (113)
T ss_pred EEEcc--cCCCEEecCC----cCccCcCCCC
Confidence 45899 8987665432 2255887764
No 294
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=33.48 E-value=34 Score=18.76 Aligned_cols=35 Identities=17% Similarity=0.554 Sum_probs=19.9
Q ss_pred CcccccccccCCCCCCc---eeeCCCCChhh-HHHHHHH
Q 048114 46 TSFICDICVEPKSTDES---FSIKGCSHSYC-TECMTKY 80 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~---~~~~~C~H~fC-~~Cl~~~ 80 (234)
....|..|..++..... +..-.-.|.|| ..|+..|
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHHhhC
Confidence 46679999988854442 44446677788 5677654
No 295
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.42 E-value=37 Score=23.68 Aligned_cols=26 Identities=23% Similarity=0.646 Sum_probs=16.6
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+|+ +|+..+..... ....||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~~---~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCE--TCQQYVTLLTQ---RVRRCPQCHG 95 (114)
T ss_pred EEEcc--cCCCeeecCCc---cCCcCcCcCC
Confidence 45899 89977654321 1256888875
No 296
>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=33.32 E-value=16 Score=21.43 Aligned_cols=29 Identities=31% Similarity=0.697 Sum_probs=16.5
Q ss_pred ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
+.|+ .|+..+...+....-.+.||.|+..
T Consensus 5 iRC~--~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCG--HCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eecc--chhHHHhhhcCccEEEEECCCCCcc
Confidence 4566 6776665533333344677776654
No 297
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=32.66 E-value=25 Score=25.82 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=8.5
Q ss_pred CcccCCCCCce
Q 048114 206 NWRRCPNCKIF 216 (234)
Q Consensus 206 ~~k~CP~C~~~ 216 (234)
.+-+||+|+.-
T Consensus 129 ~l~~Cp~C~~~ 139 (146)
T PF07295_consen 129 RLPPCPKCGHT 139 (146)
T ss_pred cCCCCCCCCCC
Confidence 35799999874
No 298
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.42 E-value=29 Score=19.02 Aligned_cols=17 Identities=29% Similarity=1.038 Sum_probs=14.8
Q ss_pred ccCccccccccccCCCC
Q 048114 157 SVCPDCNRMFCAQCKVP 173 (234)
Q Consensus 157 ~~C~~C~~~~C~~C~~~ 173 (234)
+.|..|+..||...+.+
T Consensus 13 f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 13 FKCRHCGNLFCGEHRLP 29 (39)
T ss_pred eECCccCCccccccCCc
Confidence 78999999999988764
No 299
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=32.39 E-value=31 Score=18.65 Aligned_cols=18 Identities=22% Similarity=0.650 Sum_probs=10.5
Q ss_pred cccccCCCCCCCCCChhh
Q 048114 165 MFCAQCKVPWHAGIRCAE 182 (234)
Q Consensus 165 ~~C~~C~~~~H~~~~C~~ 182 (234)
..|.+|++..|+...|..
T Consensus 3 ~~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRS 20 (36)
T ss_dssp -C-TTTSSSCS-TTT---
T ss_pred ccCcccCCCcchhhhhhh
Confidence 358888999999988874
No 300
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=32.33 E-value=51 Score=22.02 Aligned_cols=31 Identities=16% Similarity=0.344 Sum_probs=23.4
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
......||.|+..-.|..+----.|+ |++.|
T Consensus 32 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 32 QKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred HhcCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 34557999999877777777777885 88765
No 301
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=31.33 E-value=23 Score=18.29 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=6.2
Q ss_pred ccCCCCCcee
Q 048114 208 RRCPNCKIFV 217 (234)
Q Consensus 208 k~CP~C~~~i 217 (234)
.-||+|++-+
T Consensus 2 hlcpkcgvgv 11 (36)
T PF09151_consen 2 HLCPKCGVGV 11 (36)
T ss_dssp -B-TTTSSSB
T ss_pred ccCCccCceE
Confidence 3699999843
No 302
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.31 E-value=35 Score=18.97 Aligned_cols=28 Identities=18% Similarity=0.476 Sum_probs=16.9
Q ss_pred ecCCCCCCCCceecC-CCCccCcccCccccc
Q 048114 135 FYCPFKDCSALLIDD-GGEAIRESVCPDCNR 164 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~-~~~~~~~~~C~~C~~ 164 (234)
..|+ +|+..+..- .........||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCE--ECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeC--CCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4677 888644432 111245588998876
No 303
>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=31.13 E-value=23 Score=21.93 Aligned_cols=33 Identities=24% Similarity=0.574 Sum_probs=17.0
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccccccCCC
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKV 172 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 172 (234)
...|. .|...|..- .....|..||..+|..|..
T Consensus 9 ~~~C~--~C~~~F~~~----~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 9 ASNCM--ICGKKFSLF----RRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp -SB-T--TT--B-BSS----S-EEE-TTT--EEECCCS-
T ss_pred CCcCc--CcCCcCCCc----eeeEccCCCCCEECCchhC
Confidence 34677 687665331 3458999999999999975
No 304
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.82 E-value=55 Score=26.84 Aligned_cols=31 Identities=19% Similarity=0.301 Sum_probs=25.1
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
....+-||+||...+-..|=-.|.|. ||+.+
T Consensus 108 ~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 108 YRSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HhhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 35669999999998888877888885 88764
No 305
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.50 E-value=65 Score=21.51 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=23.4
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
......||.|+..-.|..+----.|+ |++.|
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred HhCCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 34557999999877777777778885 88765
No 306
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=30.42 E-value=17 Score=31.02 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=27.3
Q ss_pred CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHH
Q 048114 45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYV 81 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 81 (234)
..+.+|+|||-.++....... -|.-.+|.+|+..+-
T Consensus 72 rr~~ecpicflyyps~~n~~r-cC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNLVR-CCSETICGECFAPFG 107 (482)
T ss_pred cccccCceeeeecccccchhh-hhccchhhhheeccc
Confidence 345789999998875444444 789999999997653
No 307
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=30.40 E-value=33 Score=35.48 Aligned_cols=24 Identities=25% Similarity=0.606 Sum_probs=20.3
Q ss_pred ccCCCCCce------eeeccCCCceEec-CCCC
Q 048114 208 RRCPNCKIF------VEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~------i~k~~GCnhm~C~-C~~~ 233 (234)
..||.|+.. +...+||. +|. ||+.
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s 1735 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWS 1735 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCc
Confidence 449999999 88899997 995 9873
No 308
>PF02068 Metallothio_PEC: Plant PEC family metallothionein; InterPro: IPR000316 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , , ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as MTs from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units []. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs. Family 15 consists of planta MTs. Its members are recognised by the sequence pattern [YFH]-x(5,25)-C-[SKD]-C-[GA]-[SDPAT]-x(0,1)-C-x-[CYF] which yields all plant sequences, but also MTCU_HELPO and the non-MT ITB3_HUMAN. The taxonomic range of the members extends to planta. Planta MTs are 45-84 residue proteins, containing 17 conserved cysteines that bind 5 zinc ions. Generally, there are two Cys-rich regions (domain 1 and domain 3) separated by a Cys-poor region (domain 2) and only the domain 2 contains unusual residues. It is believed that the proteins may have a role in Zn2+ homeostasis during embryogenesis. Family 15 includes the following subfamilies: p1, p2, p2v, p3, pec, p21. ; GO: 0008270 zinc ion binding; PDB: 2L62_A 2KAK_A 2L61_A.
Probab=30.34 E-value=26 Score=22.28 Aligned_cols=26 Identities=23% Similarity=0.493 Sum_probs=8.3
Q ss_pred ccCC---CCCc--eeeeccCCCceEecCCCC
Q 048114 208 RRCP---NCKI--FVEKKEGCRYMRCSSNPQ 233 (234)
Q Consensus 208 k~CP---~C~~--~i~k~~GCnhm~C~C~~~ 233 (234)
-+|| .|+- .-.-.+|=.|++|.||.|
T Consensus 10 vPCpgG~~CrC~~~~a~~~~~~H~~C~CGEh 40 (76)
T PF02068_consen 10 VPCPGGTACRCTSSSAGGGGGDHTTCSCGEH 40 (76)
T ss_dssp SS-SSSTTSCCCS----------S-BTTTB-
T ss_pred ccCCCCCccccccccCCCCCCCcccccCCCc
Confidence 3566 3443 333456778999988865
No 309
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.32 E-value=15 Score=22.36 Aligned_cols=25 Identities=16% Similarity=0.557 Sum_probs=13.5
Q ss_pred cCCCCCce----eeeccCCCceEec-CCCC
Q 048114 209 RCPNCKIF----VEKKEGCRYMRCS-SNPQ 233 (234)
Q Consensus 209 ~CP~C~~~----i~k~~GCnhm~C~-C~~~ 233 (234)
.||.|... ..+..|=.++-|. ||++
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHH 41 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchH
Confidence 56666542 2234555666663 6664
No 310
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=29.92 E-value=75 Score=27.11 Aligned_cols=35 Identities=29% Similarity=0.642 Sum_probs=23.4
Q ss_pred ChhhHHHHHHHHHHHHhcC------CccccCCCCCCCCCCCHH
Q 048114 70 HSYCTECMTKYVASKLQEN------ITSINCPVADCKGVLEPE 106 (234)
Q Consensus 70 H~fC~~Cl~~~~~~~i~~~------~~~i~CP~~~C~~~l~~~ 106 (234)
-..|.+|+-+|+.+.-.+. .....|| .|...+-..
T Consensus 313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CP--tCRa~FCil 353 (358)
T PF10272_consen 313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCP--TCRAKFCIL 353 (358)
T ss_pred chHHHHHHHHHhhhcCCCCChhhhhcCCCCCC--CCcccceee
Confidence 3479999999997654321 1356677 888775443
No 311
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=28.86 E-value=53 Score=18.62 Aligned_cols=34 Identities=21% Similarity=0.583 Sum_probs=21.0
Q ss_pred CcccccccccCCCCCCceeeCCCCCh-hhHHHHHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHS-YCTECMTK 79 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~ 79 (234)
..+.|..|..+......+.-+.|... +|.+|+..
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 35679999874323344555678766 99999976
No 312
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.35 E-value=46 Score=17.91 Aligned_cols=24 Identities=25% Similarity=0.580 Sum_probs=16.6
Q ss_pred ccCCCCCceee-eccCCCceEe-cCCCC
Q 048114 208 RRCPNCKIFVE-KKEGCRYMRC-SSNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~-k~~GCnhm~C-~C~~~ 233 (234)
.+|+.|+.... .++| ..+| .||+.
T Consensus 9 ~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 46999998633 3455 7888 58864
No 313
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.24 E-value=1.1e+02 Score=21.93 Aligned_cols=38 Identities=21% Similarity=0.528 Sum_probs=22.3
Q ss_pred CCCeecCCCCCCCCceecC-C--CCccCcccCccccccccccC
Q 048114 131 GAQKFYCPFKDCSALLIDD-G--GEAIRESVCPDCNRMFCAQC 170 (234)
Q Consensus 131 ~~~~~~Cp~~~C~~~~~~~-~--~~~~~~~~C~~C~~~~C~~C 170 (234)
......|| .|....... + ....+...|+.|+..|=..=
T Consensus 27 ~~~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 27 QITKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred hcccCcCC--CCCccceeeECCccccccccccCCcCcceeeec
Confidence 33447899 788665221 1 12245678888887764433
No 314
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=28.15 E-value=15 Score=30.33 Aligned_cols=29 Identities=24% Similarity=0.713 Sum_probs=18.0
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccccCCC
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKV 172 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 172 (234)
-+|- .|..-+..-.. .+ -|+..||+.|-+
T Consensus 91 HfCd--~Cd~PI~IYGR----mI---PCkHvFCl~CAr 119 (389)
T KOG2932|consen 91 HFCD--RCDFPIAIYGR----MI---PCKHVFCLECAR 119 (389)
T ss_pred Eeec--ccCCcceeeec----cc---ccchhhhhhhhh
Confidence 3676 77765443221 12 478999998866
No 315
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.07 E-value=87 Score=18.33 Aligned_cols=17 Identities=29% Similarity=0.653 Sum_probs=10.1
Q ss_pred cCCCCCCCCCCCHHHHhcc
Q 048114 93 NCPVADCKGVLEPEYCRDI 111 (234)
Q Consensus 93 ~CP~~~C~~~l~~~~i~~~ 111 (234)
.|| .|+..|+.+.-..+
T Consensus 22 ~CP--lC~r~l~~e~~~~l 38 (54)
T PF04423_consen 22 CCP--LCGRPLDEEHRQEL 38 (54)
T ss_dssp E-T--TT--EE-HHHHHHH
T ss_pred cCC--CCCCCCCHHHHHHH
Confidence 899 99999998876433
No 316
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.94 E-value=67 Score=21.45 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=23.2
Q ss_pred cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
......||.|+..-.|..+----.|+ |++.|
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 33 MRAKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred HhcCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 34457999999887787777777785 87754
No 317
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.91 E-value=38 Score=21.83 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=6.1
Q ss_pred cCCCCCCCCceec
Q 048114 136 YCPFKDCSALLID 148 (234)
Q Consensus 136 ~Cp~~~C~~~~~~ 148 (234)
.|| .|+..+..
T Consensus 3 lCP--~C~v~l~~ 13 (88)
T COG3809 3 LCP--ICGVELVM 13 (88)
T ss_pred ccC--cCCceeee
Confidence 466 67654443
No 318
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.57 E-value=42 Score=19.58 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=10.4
Q ss_pred cCCcccCCCCCceee
Q 048114 204 KENWRRCPNCKIFVE 218 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~ 218 (234)
....-+||.|+..|.
T Consensus 21 ~~~~irCp~Cg~rIl 35 (49)
T COG1996 21 ETRGIRCPYCGSRIL 35 (49)
T ss_pred ccCceeCCCCCcEEE
Confidence 445578888888664
No 319
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=27.37 E-value=48 Score=24.61 Aligned_cols=25 Identities=28% Similarity=0.654 Sum_probs=17.4
Q ss_pred cccCCCCCceeeeccCCCceEe-cCCC
Q 048114 207 WRRCPNCKIFVEKKEGCRYMRC-SSNP 232 (234)
Q Consensus 207 ~k~CP~C~~~i~k~~GCnhm~C-~C~~ 232 (234)
+..||.|+..+...+. ....| +|+.
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~ 59 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNK 59 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCC
Confidence 4789999988876653 56677 3664
No 320
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=27.17 E-value=50 Score=20.12 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=20.2
Q ss_pred ccccccCCCCCCceeeCCCCChhhHH----HHHHHHHH
Q 048114 50 CDICVEPKSTDESFSIKGCSHSYCTE----CMTKYVAS 83 (234)
Q Consensus 50 C~iC~~~~~~~~~~~~~~C~H~fC~~----Cl~~~~~~ 83 (234)
|..|... ..+...-+.|++.+|.+ -...+++.
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~ 36 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYKE 36 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhcc
Confidence 5566644 23566667999999986 67777653
No 321
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=26.54 E-value=66 Score=16.98 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=14.1
Q ss_pred cCCCCCCCCceecCCCCccCcccCccccc
Q 048114 136 YCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
.|+ .|++.+..+. .--.||.|+.
T Consensus 4 ~C~--~CG~i~~g~~----~p~~CP~Cg~ 26 (34)
T cd00729 4 VCP--VCGYIHEGEE----APEKCPICGA 26 (34)
T ss_pred ECC--CCCCEeECCc----CCCcCcCCCC
Confidence 466 7887765432 1147888775
No 322
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=26.47 E-value=81 Score=17.77 Aligned_cols=31 Identities=26% Similarity=0.621 Sum_probs=20.9
Q ss_pred cccccccCCCCCCceeeCCCCCh-hhHHHHHHH
Q 048114 49 ICDICVEPKSTDESFSIKGCSHS-YCTECMTKY 80 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 80 (234)
.|.+|..++.+ ..+.-..|... +|.+|+..-
T Consensus 2 ~C~~C~~~i~g-~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIVG-VRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCcCCCCCCcC-CEEECCCCCCCcCHHHHHCcC
Confidence 58888886654 44455577644 899998744
No 323
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.45 E-value=44 Score=20.22 Aligned_cols=12 Identities=25% Similarity=1.088 Sum_probs=8.2
Q ss_pred ccCccccccccc
Q 048114 157 SVCPDCNRMFCA 168 (234)
Q Consensus 157 ~~C~~C~~~~C~ 168 (234)
-.|..||..+|.
T Consensus 19 ~NCl~CGkIiC~ 30 (57)
T PF06221_consen 19 PNCLNCGKIICE 30 (57)
T ss_pred ccccccChhhcc
Confidence 467777777764
No 324
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=26.40 E-value=1.3e+02 Score=24.44 Aligned_cols=61 Identities=15% Similarity=0.339 Sum_probs=38.4
Q ss_pred cccccccccCCCCCCceee----CCCCChhhHHHHHHHHHHHHhcC-Ccc--ccCCCCCCCCCCCHHHHhc
Q 048114 47 SFICDICVEPKSTDESFSI----KGCSHSYCTECMTKYVASKLQEN-ITS--INCPVADCKGVLEPEYCRD 110 (234)
Q Consensus 47 ~~~C~iC~~~~~~~~~~~~----~~C~H~fC~~Cl~~~~~~~i~~~-~~~--i~CP~~~C~~~l~~~~i~~ 110 (234)
..+|.+|..++...+...+ ..|+-.....||..+.... ..| ..+ =.|| .|...++-.++-.
T Consensus 182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~-e~g~~~p~eg~cp--~C~~~~~w~~lv~ 249 (276)
T KOG3005|consen 182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEV-EPGQLIPLEGMCP--KCEKFLSWTTLVD 249 (276)
T ss_pred chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhcc-CCCceeccCCCCC--chhceeeHHHHHH
Confidence 3589999998843332222 3577778889998833211 122 333 3788 9999888766554
No 325
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=26.29 E-value=43 Score=19.54 Aligned_cols=33 Identities=24% Similarity=0.685 Sum_probs=24.1
Q ss_pred CcccccccccCCCCCCceeeCCCCChhhHHHHHHH
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKY 80 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 80 (234)
.=+.|..|...+.....+. .=+..||.+|..+.
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~--~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYE--KDGKPYCKDCYQKR 57 (58)
T ss_dssp TTSBETTTTCBTTTSSEEE--ETTEEEEHHHHHHH
T ss_pred cccccCCCCCccCCCeeEe--ECCEEECHHHHhhh
Confidence 3578999999887655333 44688999998754
No 326
>PRK11032 hypothetical protein; Provisional
Probab=26.23 E-value=36 Score=25.42 Aligned_cols=13 Identities=31% Similarity=0.506 Sum_probs=9.3
Q ss_pred CCcccCCCCCcee
Q 048114 205 ENWRRCPNCKIFV 217 (234)
Q Consensus 205 ~~~k~CP~C~~~i 217 (234)
..+-+||+|+.--
T Consensus 140 ~~i~pCp~C~~~~ 152 (160)
T PRK11032 140 EVLPLCPKCGHDQ 152 (160)
T ss_pred CcCCCCCCCCCCe
Confidence 3457999998743
No 327
>PRK06386 replication factor A; Reviewed
Probab=25.93 E-value=33 Score=29.22 Aligned_cols=14 Identities=21% Similarity=0.748 Sum_probs=12.1
Q ss_pred CcccCCCCCceeee
Q 048114 206 NWRRCPNCKIFVEK 219 (234)
Q Consensus 206 ~~k~CP~C~~~i~k 219 (234)
-+++||.|+..+++
T Consensus 235 li~rCP~C~R~l~~ 248 (358)
T PRK06386 235 IFTKCSVCNKIIED 248 (358)
T ss_pred eEecCcCCCeEccC
Confidence 34899999999996
No 328
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=25.90 E-value=19 Score=24.42 Aligned_cols=33 Identities=15% Similarity=0.467 Sum_probs=21.9
Q ss_pred hcCCcccccccccCCCCCCceeeCCCCChhhHHH
Q 048114 43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTEC 76 (234)
Q Consensus 43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C 76 (234)
+....|+|.-||=....++... ..=|+.+|.+|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 3466899999987654333332 24478888887
No 329
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=25.75 E-value=68 Score=32.00 Aligned_cols=28 Identities=21% Similarity=0.655 Sum_probs=20.8
Q ss_pred hcCCcccCCCCCce-eeeccCCCceEe-cCCC
Q 048114 203 QKENWRRCPNCKIF-VEKKEGCRYMRC-SSNP 232 (234)
Q Consensus 203 ~~~~~k~CP~C~~~-i~k~~GCnhm~C-~C~~ 232 (234)
....-..||.|+.+ +.+||+| |.| .||.
T Consensus 1186 ~g~~g~~c~~cg~~~~vrngtc--~~c~~cg~ 1215 (1220)
T PRK07562 1186 QGYTGEACSECGNFTLVRNGTC--LKCDTCGS 1215 (1220)
T ss_pred CCCCCCcCCCcCCeEEEeCCee--eeccccCC
Confidence 34455789999995 5589999 678 4875
No 330
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=25.32 E-value=60 Score=27.97 Aligned_cols=33 Identities=21% Similarity=0.620 Sum_probs=25.2
Q ss_pred CCeecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114 132 AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 132 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (234)
.....|| .|+..+....-+..+...||.||+..
T Consensus 16 ~~~~~C~--eCd~~~~~P~l~~~q~A~CPRC~~~l 48 (418)
T COG2995 16 GHLILCP--ECDMLVSLPRLDSGQSAYCPRCGHTL 48 (418)
T ss_pred cceecCC--CCCceeccccCCCCCcccCCCCCCcc
Confidence 3456899 89988777766666778999998765
No 331
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.07 E-value=64 Score=16.24 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=7.5
Q ss_pred cccccccCCCCCCceeeCCCCChhhHHH
Q 048114 49 ICDICVEPKSTDESFSIKGCSHSYCTEC 76 (234)
Q Consensus 49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~C 76 (234)
.|.+|...........-..|.-.+..+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 4777776654322333345555555544
No 332
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=24.96 E-value=63 Score=18.62 Aligned_cols=28 Identities=18% Similarity=0.447 Sum_probs=15.9
Q ss_pred ecCCCCCCCCceecC-CCCccCcccCccccc
Q 048114 135 FYCPFKDCSALLIDD-GGEAIRESVCPDCNR 164 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~-~~~~~~~~~C~~C~~ 164 (234)
..|+ +|+..+... .........||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCT--ACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeC--CCCCEeEEEEecCCCCCCCCCCCCC
Confidence 3677 888744332 111134467888876
No 333
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=24.94 E-value=18 Score=28.83 Aligned_cols=31 Identities=26% Similarity=0.903 Sum_probs=9.6
Q ss_pred eecCCCCCCCCcee--cCCCCccCcccCccccccc
Q 048114 134 KFYCPFKDCSALLI--DDGGEAIRESVCPDCNRMF 166 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~--~~~~~~~~~~~C~~C~~~~ 166 (234)
..+|| .|+..-. .........+.|+.|+..|
T Consensus 31 n~yCP--~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 31 NMYCP--NCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp H---T--TT--SS-EE--------EEE-TTT--EE
T ss_pred CCcCC--CCCChhHhhccCCCccceeECCCCchHH
Confidence 35899 7886522 2233334458888887655
No 334
>PHA02325 hypothetical protein
Probab=24.80 E-value=42 Score=20.70 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=8.9
Q ss_pred CcccCCCCCce
Q 048114 206 NWRRCPNCKIF 216 (234)
Q Consensus 206 ~~k~CP~C~~~ 216 (234)
..|.||+|+.+
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 46899999984
No 335
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=24.33 E-value=58 Score=23.10 Aligned_cols=23 Identities=22% Similarity=0.687 Sum_probs=17.9
Q ss_pred cCCcccCCCCCceeeeccCCCce
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYM 226 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm 226 (234)
......|++||.+...++.|..+
T Consensus 59 AkR~~~C~~CG~~l~~~~~C~~~ 81 (124)
T PF05515_consen 59 AKRYNRCFKCGRYLHNNGNCRRN 81 (124)
T ss_pred HHHhCccccccceeecCCcCCCc
Confidence 34567999999987778888743
No 336
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.74 E-value=46 Score=28.98 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=19.6
Q ss_pred ccCCCCCceeeeccCCCceEec-CCCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRCS-SNPQL 234 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C~-C~~~F 234 (234)
-.||.|+..+ |+-|=|-..|+ ||+.+
T Consensus 351 p~Cp~Cg~~m-~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 351 PVCPRCGGRM-KSAGRNGFRCKKCGTRA 377 (421)
T ss_pred CCCCccCCch-hhcCCCCcccccccccC
Confidence 3899999976 44454589995 99854
No 337
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.69 E-value=59 Score=27.54 Aligned_cols=25 Identities=20% Similarity=0.639 Sum_probs=18.5
Q ss_pred CcccccccccCCCCCCceeeCCCCChhh
Q 048114 46 TSFICDICVEPKSTDESFSIKGCSHSYC 73 (234)
Q Consensus 46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC 73 (234)
....|.||.++.. + ..+.+|||.-|
T Consensus 304 ~p~lcVVcl~e~~--~-~~fvpcGh~cc 328 (355)
T KOG1571|consen 304 QPDLCVVCLDEPK--S-AVFVPCGHVCC 328 (355)
T ss_pred CCCceEEecCCcc--c-eeeecCCcEEE
Confidence 3556999999874 3 44569999955
No 338
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.66 E-value=61 Score=30.30 Aligned_cols=26 Identities=27% Similarity=0.556 Sum_probs=18.8
Q ss_pred ccCCCCCceeeeccCCCceEe-cCCCC
Q 048114 208 RRCPNCKIFVEKKEGCRYMRC-SSNPQ 233 (234)
Q Consensus 208 k~CP~C~~~i~k~~GCnhm~C-~C~~~ 233 (234)
-.||+|...+.-...=+.|.| .||+.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCC
Confidence 479999987664334478999 49875
No 339
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.13 E-value=57 Score=19.65 Aligned_cols=36 Identities=25% Similarity=0.418 Sum_probs=25.5
Q ss_pred cccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHHH
Q 048114 91 SINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAV 128 (234)
Q Consensus 91 ~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~ 128 (234)
...|| .|+.......=..+-+.+-+.+|...+....
T Consensus 17 k~~CP--~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 17 KEICP--VCGGKTKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred cccCc--CCCCCCCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 44678 7887766666566677788888888776543
No 340
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=23.11 E-value=97 Score=25.30 Aligned_cols=60 Identities=13% Similarity=0.468 Sum_probs=35.3
Q ss_pred CCcccccccccCCCC---CCcee---eCCCCChhhHHHHHH-HH-HHHHhc--CCccccCCCCCCCCCCCHH
Q 048114 45 ETSFICDICVEPKST---DESFS---IKGCSHSYCTECMTK-YV-ASKLQE--NITSINCPVADCKGVLEPE 106 (234)
Q Consensus 45 ~~~~~C~iC~~~~~~---~~~~~---~~~C~H~fC~~Cl~~-~~-~~~i~~--~~~~i~CP~~~C~~~l~~~ 106 (234)
.+.+.|.+|--.+.. -.+.. .++|...+|-.=|-+ |+ +-.|+. |..++.|| .|...+...
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~--hC~kAFADR 228 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCP--HCGKAFADR 228 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCC--cccchhcch
Confidence 567889999766631 12211 136666666554443 22 223333 67799999 898887764
No 341
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.78 E-value=31 Score=28.39 Aligned_cols=26 Identities=35% Similarity=0.746 Sum_probs=13.1
Q ss_pred ccCCCCCce-----eeecc--CCCceEec-CCCC
Q 048114 208 RRCPNCKIF-----VEKKE--GCRYMRCS-SNPQ 233 (234)
Q Consensus 208 k~CP~C~~~-----i~k~~--GCnhm~C~-C~~~ 233 (234)
..||-||.. |...+ |=-+++|. |+++
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~ 206 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTE 206 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--E
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCe
Confidence 799999984 33333 78999996 9986
No 342
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.73 E-value=64 Score=22.59 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=15.4
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+|. +|+..+..... ....||.||.
T Consensus 71 ~~~C~--~Cg~~~~~~~~---~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECK--DCSHVFKPNAL---DYGVCEKCHS 96 (117)
T ss_pred EEEhh--hCCCccccCCc---cCCcCcCCCC
Confidence 35888 88866554321 1134887765
No 343
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=22.16 E-value=18 Score=28.72 Aligned_cols=40 Identities=28% Similarity=0.684 Sum_probs=27.7
Q ss_pred ecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChh
Q 048114 135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCA 181 (234)
Q Consensus 135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~ 181 (234)
..||.+.|...... .+.+.|..|+..+|...+.+. +++|.
T Consensus 99 ~kc~~~~c~k~~~~-----~~~~~c~~c~~~~c~khr~~~--dhsc~ 138 (250)
T KOG3183|consen 99 NKCPVPRCKKTLTL-----ANKITCSKCGRNFCLKHRHPL--DHSCN 138 (250)
T ss_pred ccCCchhhHHHHHH-----HHhhhhHhhcchhhhhccCCC--Cchhh
Confidence 35888888865443 234899999999998776541 34565
No 344
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=22.03 E-value=1.2e+02 Score=28.55 Aligned_cols=20 Identities=10% Similarity=-0.021 Sum_probs=13.8
Q ss_pred cCCHHHHHHHHHHHHHHHHh
Q 048114 111 ILPEDVFNRWGNALCEAVIL 130 (234)
Q Consensus 111 ~l~~~~~~~~~~~~~~~~~~ 130 (234)
.|+....++|+.+..+.+..
T Consensus 1088 ~l~~a~kq~ye~La~~iFsk 1107 (1189)
T KOG2041|consen 1088 ELDDAEKQEYENLAFRIFSK 1107 (1189)
T ss_pred hCCHHHHHHHHHHHHHHhcc
Confidence 46677788888877765544
No 345
>PLN02436 cellulose synthase A
Probab=21.85 E-value=75 Score=31.20 Aligned_cols=50 Identities=28% Similarity=0.723 Sum_probs=32.6
Q ss_pred cccccccccCCC---CCCcee-eCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114 47 SFICDICVEPKS---TDESFS-IKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104 (234)
Q Consensus 47 ~~~C~iC~~~~~---~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 104 (234)
...|+||.+++. ..+.|. .-.|+=..|+.|. +|-. ++| .-.|| .|+....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg--~~~Cp--qckt~Y~ 89 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REG--NQACP--QCKTRYK 89 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcC--CccCc--ccCCchh
Confidence 558999999973 223343 3357888999999 4432 234 34789 7876544
No 346
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.74 E-value=66 Score=19.88 Aligned_cols=30 Identities=17% Similarity=0.419 Sum_probs=21.9
Q ss_pred eecCCCCCCCCceecCCCCccCcccCccccccccccCCC
Q 048114 134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKV 172 (234)
Q Consensus 134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 172 (234)
...|..++|...- .+.|..|.+.+|+.+..
T Consensus 27 ~~~C~~~gC~~~s---------~I~C~~Ckk~~Cf~Hfi 56 (63)
T PF04236_consen 27 AGDCDITGCNNTS---------FIRCAYCKKSLCFNHFI 56 (63)
T ss_pred cCcCCCCCCCCcC---------EEEccccCCccccccee
Confidence 3467766777542 27899999999998765
No 347
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=21.40 E-value=51 Score=22.88 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=10.2
Q ss_pred ccCCCCCceeee
Q 048114 208 RRCPNCKIFVEK 219 (234)
Q Consensus 208 k~CP~C~~~i~k 219 (234)
--||+|+.+++-
T Consensus 75 yyCP~Cgt~lev 86 (112)
T PF08882_consen 75 YYCPGCGTQLEV 86 (112)
T ss_pred EECCCCcceeEE
Confidence 379999999875
No 348
>PRK02935 hypothetical protein; Provisional
Probab=21.14 E-value=47 Score=22.80 Aligned_cols=19 Identities=21% Similarity=0.539 Sum_probs=12.8
Q ss_pred cccCCCCCcee---eeccCCCc
Q 048114 207 WRRCPNCKIFV---EKKEGCRY 225 (234)
Q Consensus 207 ~k~CP~C~~~i---~k~~GCnh 225 (234)
.-.||+|+... -|.+.|.|
T Consensus 70 qV~CP~C~K~TKmLGrvD~CM~ 91 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVDACMH 91 (110)
T ss_pred eeECCCCCchhhhccceeecCc
Confidence 35899999854 35666654
No 349
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.03 E-value=65 Score=15.61 Aligned_cols=22 Identities=14% Similarity=0.428 Sum_probs=13.8
Q ss_pred HHHHHHHHhcCCccccCCCCCCCCCC
Q 048114 78 TKYVASKLQENITSINCPVADCKGVL 103 (234)
Q Consensus 78 ~~~~~~~i~~~~~~i~CP~~~C~~~l 103 (234)
..++... .+..+..|| .|+..+
T Consensus 3 ~~H~~~H--~~~k~~~C~--~C~k~F 24 (26)
T PF13465_consen 3 RRHMRTH--TGEKPYKCP--YCGKSF 24 (26)
T ss_dssp HHHHHHH--SSSSSEEES--SSSEEE
T ss_pred HHHhhhc--CCCCCCCCC--CCcCee
Confidence 4455543 456688999 787543
No 350
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=20.99 E-value=1.2e+02 Score=18.51 Aligned_cols=14 Identities=21% Similarity=0.589 Sum_probs=10.3
Q ss_pred ccccCCCCCCCCCCCH
Q 048114 90 TSINCPVADCKGVLEP 105 (234)
Q Consensus 90 ~~i~CP~~~C~~~l~~ 105 (234)
.|++|+ .|+.++..
T Consensus 3 iPVRCF--TCGkvi~~ 16 (60)
T PF01194_consen 3 IPVRCF--TCGKVIGN 16 (60)
T ss_dssp -SSS-S--TTTSBTCG
T ss_pred CceecC--CCCCChhH
Confidence 589999 99998873
No 351
>PF10530 Toxin_35: Toxin with inhibitor cystine knot ICK or Knottin scaffold; InterPro: IPR019553 Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulphide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of Cupiennius salei (Wandering spider) venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels []. Interestingly, the omega-toxins from Phoneutria nigriventer (Brazilian armed spider) venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulphide bond arrangement. suggested that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 these toxins [].
Probab=20.77 E-value=50 Score=15.86 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=8.2
Q ss_pred eccCCCceEecC
Q 048114 219 KKEGCRYMRCSS 230 (234)
Q Consensus 219 k~~GCnhm~C~C 230 (234)
|++-|-.|+|.|
T Consensus 12 k~gCC~~~~C~C 23 (23)
T PF10530_consen 12 KHGCCFKWKCNC 23 (23)
T ss_pred CCCceeeeEecC
Confidence 556677788765
No 352
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.68 E-value=84 Score=23.87 Aligned_cols=32 Identities=22% Similarity=0.535 Sum_probs=19.2
Q ss_pred CCCeecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114 131 GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165 (234)
Q Consensus 131 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (234)
.+....|| .|...+..+.... ..+.||.||..
T Consensus 110 ~~~~y~C~--~~~~r~sfdeA~~-~~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCP--NCHVKYSFDEAME-LGFTCPKCGED 141 (176)
T ss_pred cCCceeCC--CCCCcccHHHHHH-hCCCCCCCCch
Confidence 44557897 7776666553222 23778777653
No 353
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=20.64 E-value=1.2e+02 Score=18.06 Aligned_cols=25 Identities=28% Similarity=0.818 Sum_probs=15.4
Q ss_pred CCCeecCCCCCCCCceecCCCCccCcccCccccc
Q 048114 131 GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNR 164 (234)
Q Consensus 131 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (234)
..+...|| .|+.+.. ....|+.||+
T Consensus 23 ~~~l~~c~--~cg~~~~-------~H~vc~~cG~ 47 (56)
T PF01783_consen 23 APNLVKCP--NCGEPKL-------PHRVCPSCGY 47 (56)
T ss_dssp TTSEEESS--SSSSEES-------TTSBCTTTBB
T ss_pred ccceeeec--cCCCEec-------ccEeeCCCCe
Confidence 34667888 7776543 2266777764
No 354
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.55 E-value=83 Score=23.57 Aligned_cols=16 Identities=25% Similarity=0.519 Sum_probs=11.5
Q ss_pred CCeecCCCCCCCCceecC
Q 048114 132 AQKFYCPFKDCSALLIDD 149 (234)
Q Consensus 132 ~~~~~Cp~~~C~~~~~~~ 149 (234)
+....|| .|+..+...
T Consensus 95 ~e~~RCp--~CN~~L~~v 110 (165)
T COG1656 95 PEFSRCP--ECNGELEKV 110 (165)
T ss_pred cccccCc--ccCCEeccC
Confidence 3456899 999876654
No 355
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=20.54 E-value=86 Score=25.43 Aligned_cols=30 Identities=17% Similarity=0.555 Sum_probs=22.5
Q ss_pred cCCcccCCCCCceeeeccCCCceEecCCCCC
Q 048114 204 KENWRRCPNCKIFVEKKEGCRYMRCSSNPQL 234 (234)
Q Consensus 204 ~~~~k~CP~C~~~i~k~~GCnhm~C~C~~~F 234 (234)
....|.||+|+-.+---..|.. +|.||..|
T Consensus 231 nk~ck~C~nC~La~HPFtnC~s-~CvCG~~f 260 (285)
T PF03563_consen 231 NKSCKKCKNCGLAYHPFTNCGS-HCVCGMKF 260 (285)
T ss_pred HHHhhhCcccCeeccCCCCCCC-eeeccccc
Confidence 4557999999998866666653 68888766
No 356
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=20.06 E-value=36 Score=19.64 Aligned_cols=17 Identities=29% Similarity=0.682 Sum_probs=12.4
Q ss_pred cccccCCCCCCCCCChh
Q 048114 165 MFCAQCKVPWHAGIRCA 181 (234)
Q Consensus 165 ~~C~~C~~~~H~~~~C~ 181 (234)
.+|+.|+..-|....|.
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 57788888788776664
No 357
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=20.04 E-value=72 Score=18.54 Aligned_cols=29 Identities=14% Similarity=0.322 Sum_probs=19.2
Q ss_pred CcccCCCCCceeeecc--------CCCceEecCCCCC
Q 048114 206 NWRRCPNCKIFVEKKE--------GCRYMRCSSNPQL 234 (234)
Q Consensus 206 ~~k~CP~C~~~i~k~~--------GCnhm~C~C~~~F 234 (234)
.+-.||+|+.-..-++ .=-+=+|+||..+
T Consensus 12 kY~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfni 48 (49)
T PF12677_consen 12 KYCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFNI 48 (49)
T ss_pred hhccCcccCCcEeecCcceEEEeccceeeeecccccc
Confidence 3679999998655443 2334578887653
Done!